APA and expression effect size relationship in total

Last updated: 2020-05-28

Checks: 7 0

Knit directory: Comparative_APA/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.6.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20190902)

The command set.seed(20190902) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 1cc5ab7

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    code/chimp_log/
    Ignored:    code/human_log/
    Ignored:    data/.DS_Store
    Ignored:    data/TrialFiltersMeta.txt.sb-9845453e-R58Y0Q/
    Ignored:    data/mediation_prot/
    Ignored:    data/metadata_HCpanel.txt.sb-284518db-RGf0kd/
    Ignored:    data/metadata_HCpanel.txt.sb-a5794dd2-i594qs/
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  ._.DS_Store
    Untracked:  Chimp/
    Untracked:  Human/
    Untracked:  analysis/AREstabilityScores.Rmd
    Untracked:  analysis/AllLoc_effectSizeCor.Rmd
    Untracked:  analysis/Conservation_bydAPAset.Rmd
    Untracked:  analysis/CrossChimpThreePrime.Rmd
    Untracked:  analysis/DiffTransProtvsExpression.Rmd
    Untracked:  analysis/DiffUsedUTR.Rmd
    Untracked:  analysis/GvizPlots.Rmd
    Untracked:  analysis/HandC.TvN
    Untracked:  analysis/PhenotypeOverlap10.Rmd
    Untracked:  analysis/annotationBias.Rmd
    Untracked:  analysis/assessReadQual.Rmd
    Untracked:  analysis/diffExpressionPantro6.Rmd
    Untracked:  code/._AlignmentScores.sh
    Untracked:  code/._BothFCMM.sh
    Untracked:  code/._BothFCMMPrim.sh
    Untracked:  code/._BothFCnewOInclusive.sh
    Untracked:  code/._ChimpStarMM2.sh
    Untracked:  code/._ClassifyLeafviz.sh
    Untracked:  code/._ClosestorthoEx.sh
    Untracked:  code/._Config_chimp.yaml
    Untracked:  code/._Config_chimp_full.yaml
    Untracked:  code/._Config_human.yaml
    Untracked:  code/._ConvertJunc2Bed.sh
    Untracked:  code/._CountNucleotides.py
    Untracked:  code/._CrossMapChimpRNA.sh
    Untracked:  code/._CrossMapThreeprime.sh
    Untracked:  code/._DiffSplice.sh
    Untracked:  code/._DiffSplicePlots.sh
    Untracked:  code/._DiffSplicePlots_gencode.sh
    Untracked:  code/._DiffSplice_gencode.sh
    Untracked:  code/._DiffSplice_removebad.sh
    Untracked:  code/._Filter255MM.sh
    Untracked:  code/._FilterPrimSec.sh
    Untracked:  code/._FindIntronForDomPAS.sh
    Untracked:  code/._FindIntronForDomPAS_DF.sh
    Untracked:  code/._GetMAPQscore.py
    Untracked:  code/._GetSecondaryMap.py
    Untracked:  code/._Lift5perPAS.sh
    Untracked:  code/._LiftFinalChimpJunc2Human.sh
    Untracked:  code/._LiftOrthoPAS2chimp.sh
    Untracked:  code/._MapBadSamples.sh
    Untracked:  code/._MismatchNumbers.sh
    Untracked:  code/._PAS_ATTAAA.sh
    Untracked:  code/._PAS_ATTAAA_df.sh
    Untracked:  code/._PAS_seqExpanded.sh
    Untracked:  code/._PASsequences.sh
    Untracked:  code/._PASsequences_DF.sh
    Untracked:  code/._PlotNuclearUsagebySpecies.R
    Untracked:  code/._PlotNuclearUsagebySpecies_DF.R
    Untracked:  code/._QuantMergedClusters.sh
    Untracked:  code/._RNATranscriptDTplot.sh
    Untracked:  code/._ReverseLiftFilter.R
    Untracked:  code/._RunFixLeafCluster.sh
    Untracked:  code/._RunNegMCMediation.sh
    Untracked:  code/._RunNegMCMediationDF.sh
    Untracked:  code/._RunPosMCMediationDF.err
    Untracked:  code/._RunPosMCMediationDF.sh
    Untracked:  code/._SAF2Bed.py
    Untracked:  code/._Snakefile
    Untracked:  code/._SnakefilePAS
    Untracked:  code/._SnakefilePASfilt
    Untracked:  code/._SortIndexBadSamples.sh
    Untracked:  code/._StarMM2.sh
    Untracked:  code/._TestFC.sh
    Untracked:  code/._assignPeak2Intronicregion
    Untracked:  code/._assignPeak2Intronicregion.sh
    Untracked:  code/._bed215upbed.py
    Untracked:  code/._bed2Bedbothstrand.py
    Untracked:  code/._bed2SAF_gen.py
    Untracked:  code/._buildIndecpantro5
    Untracked:  code/._buildIndecpantro5.sh
    Untracked:  code/._buildLeafviz.sh
    Untracked:  code/._buildLeafviz_leadAnno.sh
    Untracked:  code/._buildStarIndex.sh
    Untracked:  code/._chimpChromprder.sh
    Untracked:  code/._chimpMultiCov.sh
    Untracked:  code/._chimpMultiCov255.sh
    Untracked:  code/._chimpMultiCovInclusive.sh
    Untracked:  code/._chooseSignalSite.py
    Untracked:  code/._cleanbed2saf.py
    Untracked:  code/._cluster.json
    Untracked:  code/._cluster2bed.py
    Untracked:  code/._clusterLiftReverse.sh
    Untracked:  code/._clusterLiftReverse_removebad.sh
    Untracked:  code/._clusterLiftprimary.sh
    Untracked:  code/._clusterLiftprimary_removebad.sh
    Untracked:  code/._converBam2Junc.sh
    Untracked:  code/._converBam2Junc_removeBad.sh
    Untracked:  code/._extraSnakefiltpas
    Untracked:  code/._extractPhyloReg.py
    Untracked:  code/._extractPhyloRegGene.py
    Untracked:  code/._extractPhylopGeneral.ph
    Untracked:  code/._extractPhylopGeneral.py
    Untracked:  code/._extractPhylopReg200down.py
    Untracked:  code/._extractPhylopReg200up.py
    Untracked:  code/._filter5percPAS.py
    Untracked:  code/._filterNumChroms.py
    Untracked:  code/._filterPASforMP.py
    Untracked:  code/._filterPostLift.py
    Untracked:  code/._filterPrimaryread.py
    Untracked:  code/._filterSecondaryread.py
    Untracked:  code/._fixExonFC.py
    Untracked:  code/._fixFCheadforExp.py
    Untracked:  code/._fixLeafCluster.py
    Untracked:  code/._fixLiftedJunc.py
    Untracked:  code/._fixUTRexonanno.py
    Untracked:  code/._formathg38Anno.py
    Untracked:  code/._formatpantro6Anno.py
    Untracked:  code/._getRNAseqMapStats.sh
    Untracked:  code/._hg19MapStats.sh
    Untracked:  code/._humanChromorder.sh
    Untracked:  code/._humanMultiCov.sh
    Untracked:  code/._humanMultiCov255.sh
    Untracked:  code/._humanMultiCov_inclusive.sh
    Untracked:  code/._intersectLiftedPAS.sh
    Untracked:  code/._liftJunctionFiles.sh
    Untracked:  code/._liftPAS19to38.sh
    Untracked:  code/._liftedchimpJunc2human.sh
    Untracked:  code/._makeNuclearDapaplots.sh
    Untracked:  code/._makeNuclearDapaplots_DF.sh
    Untracked:  code/._makeSamplyGroupsHuman_TvN.py
    Untracked:  code/._mapRNAseqhg19.sh
    Untracked:  code/._mapRNAseqhg19_newPipeline.sh
    Untracked:  code/._maphg19.sh
    Untracked:  code/._maphg19_subjunc.sh
    Untracked:  code/._mediation_test.R
    Untracked:  code/._mergeChimp3prime_inhg38.sh
    Untracked:  code/._mergeandBWRNAseq.sh
    Untracked:  code/._mergedBam2BW.sh
    Untracked:  code/._nameClusters.py
    Untracked:  code/._negativeMediation_montecarlo.R
    Untracked:  code/._negativeMediation_montecarloDF.R
    Untracked:  code/._numMultimap.py
    Untracked:  code/._overlapMMandOrthoexon.sh
    Untracked:  code/._overlapPASandOrthoexon.sh
    Untracked:  code/._overlapapaQTLPAS.sh
    Untracked:  code/._parseHg38.py
    Untracked:  code/._postiveMediation_montecarlo_DF.R
    Untracked:  code/._prepareCleanLiftedFC_5perc4LC.py
    Untracked:  code/._prepareLeafvizAnno.sh
    Untracked:  code/._preparePAS4lift.py
    Untracked:  code/._primaryLift.sh
    Untracked:  code/._processhg38exons.py
    Untracked:  code/._quantJunc.sh
    Untracked:  code/._quantJunc_TEST.sh
    Untracked:  code/._quantJunc_removeBad.sh
    Untracked:  code/._quantLiftedPASPrimary.sh
    Untracked:  code/._quantMerged_seperatly.sh
    Untracked:  code/._recLiftchim2human.sh
    Untracked:  code/._revLiftPAShg38to19.sh
    Untracked:  code/._reverseLift.sh
    Untracked:  code/._runCheckReverseLift.sh
    Untracked:  code/._runChimpDiffIso.sh
    Untracked:  code/._runCountNucleotides.sh
    Untracked:  code/._runFilterNumChroms.sh
    Untracked:  code/._runHumanDiffIso.sh
    Untracked:  code/._runNuclearDiffIso_DF.sh
    Untracked:  code/._runNuclearDifffIso.sh
    Untracked:  code/._runTotalDiffIso.sh
    Untracked:  code/._run_chimpverifybam.sh
    Untracked:  code/._run_verifyBam.sh
    Untracked:  code/._snakemake.batch
    Untracked:  code/._snakemakePAS.batch
    Untracked:  code/._snakemakePASchimp.batch
    Untracked:  code/._snakemakePAShuman.batch
    Untracked:  code/._snakemake_chimp.batch
    Untracked:  code/._snakemake_human.batch
    Untracked:  code/._snakemakefiltPAS.batch
    Untracked:  code/._snakemakefiltPAS_chimp
    Untracked:  code/._snakemakefiltPAS_chimp.sh
    Untracked:  code/._snakemakefiltPAS_human.sh
    Untracked:  code/._spliceSite2Fasta.py
    Untracked:  code/._submit-snakemake-chimp.sh
    Untracked:  code/._submit-snakemake-human.sh
    Untracked:  code/._submit-snakemakePAS-chimp.sh
    Untracked:  code/._submit-snakemakePAS-human.sh
    Untracked:  code/._submit-snakemakefiltPAS-chimp.sh
    Untracked:  code/._submit-snakemakefiltPAS-human.sh
    Untracked:  code/._subset_diffisopheno_Nuclear_HvC.py
    Untracked:  code/._subset_diffisopheno_Nuclear_HvC_DF.py
    Untracked:  code/._subset_diffisopheno_Total_HvC.py
    Untracked:  code/._threeprimeOrthoFC.sh
    Untracked:  code/._transcriptDTplotsNuclear.sh
    Untracked:  code/._verifyBam4973.sh
    Untracked:  code/._verifyBam4973inHuman.sh
    Untracked:  code/._wrap_chimpverifybam.sh
    Untracked:  code/._wrap_verifyBam.sh
    Untracked:  code/._writeMergecode.py
    Untracked:  code/.snakemake/
    Untracked:  code/ALLPAS_sequenceDF.err
    Untracked:  code/ALLPAS_sequenceDF.out
    Untracked:  code/AlignmentScores.err
    Untracked:  code/AlignmentScores.out
    Untracked:  code/AlignmentScores.sh
    Untracked:  code/BothFCMM.err
    Untracked:  code/BothFCMM.out
    Untracked:  code/BothFCMM.sh
    Untracked:  code/BothFCMMPrim.err
    Untracked:  code/BothFCMMPrim.out
    Untracked:  code/BothFCMMPrim.sh
    Untracked:  code/BothFCnewOInclusive.sh
    Untracked:  code/BothFCnewOInclusive.sh.err
    Untracked:  code/BothFCnewOInclusive.sh.out
    Untracked:  code/ChimpStarMM2.err
    Untracked:  code/ChimpStarMM2.out
    Untracked:  code/ChimpStarMM2.sh
    Untracked:  code/ClassifyLeafviz.sh
    Untracked:  code/ClosestorthoEx.err
    Untracked:  code/ClosestorthoEx.out
    Untracked:  code/ClosestorthoEx.sh
    Untracked:  code/Config_chimp.yaml
    Untracked:  code/Config_chimp_full.yaml
    Untracked:  code/Config_human.yaml
    Untracked:  code/ConvertJunc2Bed.err
    Untracked:  code/ConvertJunc2Bed.out
    Untracked:  code/ConvertJunc2Bed.sh
    Untracked:  code/CountNucleotides.py
    Untracked:  code/CrossMapChimpRNA.sh
    Untracked:  code/CrossMapThreeprime.sh
    Untracked:  code/CrossmapChimp3prime.err
    Untracked:  code/CrossmapChimp3prime.out
    Untracked:  code/CrossmapChimpRNA.err
    Untracked:  code/CrossmapChimpRNA.out
    Untracked:  code/DTUTR.sh
    Untracked:  code/DiffDom_RNAmotif_4.err
    Untracked:  code/DiffDom_RNAmotif_4.out
    Untracked:  code/DiffDom_RNAmotif_4.sh
    Untracked:  code/DiffDom_RNAmotif_4_splitDE.err
    Untracked:  code/DiffDom_RNAmotif_4_splitDE.out
    Untracked:  code/DiffDom_RNAmotif_4_splitDE.sh
    Untracked:  code/DiffSplice.err
    Untracked:  code/DiffSplice.out
    Untracked:  code/DiffSplice.sh
    Untracked:  code/DiffSplicePlots.err
    Untracked:  code/DiffSplicePlots.out
    Untracked:  code/DiffSplicePlots.sh
    Untracked:  code/DiffSplicePlots_gencode.sh
    Untracked:  code/DiffSplice_gencode.sh
    Untracked:  code/DiffSplice_removebad.err
    Untracked:  code/DiffSplice_removebad.out
    Untracked:  code/DiffSplice_removebad.sh
    Untracked:  code/Filter255.err
    Untracked:  code/Filter255.out
    Untracked:  code/Filter255MM.sh
    Untracked:  code/FilterPrimSec.err
    Untracked:  code/FilterPrimSec.out
    Untracked:  code/FilterPrimSec.sh
    Untracked:  code/FilterReverseLift.err
    Untracked:  code/FilterReverseLift.out
    Untracked:  code/FindDomXCutoff.py
    Untracked:  code/FindIntronForDomPAS.err
    Untracked:  code/FindIntronForDomPAS.out
    Untracked:  code/FindIntronForDomPAS.sh
    Untracked:  code/FindIntronForDomPAS_DF.sh
    Untracked:  code/GencodeDiffSplice.err
    Untracked:  code/GencodeDiffSplice.out
    Untracked:  code/GetMAPQscore.py
    Untracked:  code/GetSecondaryMap.py
    Untracked:  code/GetTopminus2Usage.py
    Untracked:  code/H3K36me3DTplot.err
    Untracked:  code/H3K36me3DTplot.out
    Untracked:  code/H3K36me3DTplot.sh
    Untracked:  code/H3K36me3DTplot_DiffIso.err
    Untracked:  code/H3K36me3DTplot_DiffIso.out
    Untracked:  code/H3K36me3DTplot_DiffIso.sh
    Untracked:  code/H3K36me3DTplot_Specific.err
    Untracked:  code/H3K36me3DTplot_Specific.out
    Untracked:  code/H3K36me3DTplot_Specific.sh
    Untracked:  code/H3K36me3DTplot_distalPAS.err
    Untracked:  code/H3K36me3DTplot_distalPAS.out
    Untracked:  code/H3K36me3DTplot_distalPAS.sh
    Untracked:  code/H3K36me3DTplot_transcript.err
    Untracked:  code/H3K36me3DTplot_transcript.out
    Untracked:  code/H3K36me3DTplot_transcript.sh
    Untracked:  code/H3K36me3DTplotwide.err
    Untracked:  code/H3K36me3DTplotwide.out
    Untracked:  code/H3K36me3DTplotwide.sh
    Untracked:  code/H3K9me3DTplot_transcript.err
    Untracked:  code/H3K9me3DTplot_transcript.out
    Untracked:  code/H3K9me3DTplot_transcript.sh
    Untracked:  code/H3K9me3_processandDT.sh
    Untracked:  code/HchromOrder.err
    Untracked:  code/HchromOrder.out
    Untracked:  code/InfoContentShannon.py
    Untracked:  code/InfoContentbyInd.py
    Untracked:  code/IntersectMMandOrtho.err
    Untracked:  code/IntersectMMandOrtho.out
    Untracked:  code/IntersectPASandOrtho.err
    Untracked:  code/IntersectPASandOrtho.out
    Untracked:  code/JunctionLift.err
    Untracked:  code/JunctionLift.out
    Untracked:  code/JunctionLiftFinalChimp.err
    Untracked:  code/JunctionLiftFinalChimp.out
    Untracked:  code/Lift5perPAS.sh
    Untracked:  code/Lift5perPASbed.err
    Untracked:  code/Lift5perPASbed.out
    Untracked:  code/LiftClustersFirst.err
    Untracked:  code/LiftClustersFirst.out
    Untracked:  code/LiftClustersFirst_remove.err
    Untracked:  code/LiftClustersFirst_remove.out
    Untracked:  code/LiftClustersSecond.err
    Untracked:  code/LiftClustersSecond.out
    Untracked:  code/LiftClustersSecond_remove.err
    Untracked:  code/LiftClustersSecond_remove.out
    Untracked:  code/LiftFinalChimpJunc2Human.sh
    Untracked:  code/LiftOrthoPAS2chimp.sh
    Untracked:  code/LiftorthoPAS.err
    Untracked:  code/LiftorthoPASt.out
    Untracked:  code/Log.out
    Untracked:  code/MapBadSamples.err
    Untracked:  code/MapBadSamples.out
    Untracked:  code/MapBadSamples.sh
    Untracked:  code/MapStats.err
    Untracked:  code/MapStats.out
    Untracked:  code/MaxEntCode/
    Untracked:  code/MergeClusters.err
    Untracked:  code/MergeClusters.out
    Untracked:  code/MergeClusters.sh
    Untracked:  code/MismatchNumbers.err
    Untracked:  code/MismatchNumbers.out
    Untracked:  code/MismatchNumbers.sh
    Untracked:  code/NuclearDTUTR.err
    Untracked:  code/NuclearDTUTRt.out
    Untracked:  code/NuclearPlotsDEandDiffDom_4.err
    Untracked:  code/NuclearPlotsDEandDiffDom_4.out
    Untracked:  code/NuclearPlotsDEandDiffDom_4.sh
    Untracked:  code/PAS_ATTAAA.err
    Untracked:  code/PAS_ATTAAA.out
    Untracked:  code/PAS_ATTAAA.sh
    Untracked:  code/PAS_ATTAAADF.err
    Untracked:  code/PAS_ATTAAADF.out
    Untracked:  code/PAS_ATTAAA_df.sh
    Untracked:  code/PAS_seqExpanded.sh
    Untracked:  code/PAS_sequence.err
    Untracked:  code/PAS_sequence.out
    Untracked:  code/PAS_sequenceDF.err
    Untracked:  code/PAS_sequenceDF.out
    Untracked:  code/PASexpanded_sequenceDF.err
    Untracked:  code/PASexpanded_sequenceDF.out
    Untracked:  code/PASsequences.sh
    Untracked:  code/PASsequences_DF.sh
    Untracked:  code/PlotNuclearUsagebySpecies.R
    Untracked:  code/PlotNuclearUsagebySpecies_DF.R
    Untracked:  code/PlotNuclearUsagebySpecies_DF_4DIC.R
    Untracked:  code/PlotNuclearUsagebySpecies_DF_DEout.R
    Untracked:  code/QuantMergeClusters
    Untracked:  code/QuantMergeClusters.err
    Untracked:  code/QuantMergeClusters.out
    Untracked:  code/QuantMergedClusters.sh
    Untracked:  code/RNATranscriptDTplot.err
    Untracked:  code/RNATranscriptDTplot.out
    Untracked:  code/RNATranscriptDTplot.sh
    Untracked:  code/RNAmotif_PAS.err
    Untracked:  code/RNAmotif_PAS.out
    Untracked:  code/RNAmotif_PAS.sh
    Untracked:  code/RNAmotif_PAS_chimp.err
    Untracked:  code/RNAmotif_PAS_chimp.out
    Untracked:  code/RNAmotif_PAS_chimp.sh
    Untracked:  code/Rev_liftoverPAShg19to38.err
    Untracked:  code/Rev_liftoverPAShg19to38.out
    Untracked:  code/ReverseLiftFilter.R
    Untracked:  code/RunFixCluster.err
    Untracked:  code/RunFixCluster.out
    Untracked:  code/RunFixLeafCluster.sh
    Untracked:  code/RunNegMCMediation.err
    Untracked:  code/RunNegMCMediation.sh
    Untracked:  code/RunNegMCMediationDF.err
    Untracked:  code/RunNegMCMediationDF.out
    Untracked:  code/RunNegMCMediationDF.sh
    Untracked:  code/RunNegMCMediationr.out
    Untracked:  code/RunNewDom.err
    Untracked:  code/RunNewDom.out
    Untracked:  code/RunPosMCMediation.err
    Untracked:  code/RunPosMCMediation.sh
    Untracked:  code/RunPosMCMediationDF.err
    Untracked:  code/RunPosMCMediationDF.out
    Untracked:  code/RunPosMCMediationDF.sh
    Untracked:  code/RunPosMCMediationr.out
    Untracked:  code/SAF215upbed_gen.py
    Untracked:  code/SAF2Bed.py
    Untracked:  code/Snakefile
    Untracked:  code/SnakefilePAS
    Untracked:  code/SnakefilePASfilt
    Untracked:  code/SortIndexBadSamples.err
    Untracked:  code/SortIndexBadSamples.out
    Untracked:  code/SortIndexBadSamples.sh
    Untracked:  code/StarMM2.err
    Untracked:  code/StarMM2.out
    Untracked:  code/StarMM2.sh
    Untracked:  code/TestFC.err
    Untracked:  code/TestFC.out
    Untracked:  code/TestFC.sh
    Untracked:  code/TotalTranscriptDTplot.err
    Untracked:  code/TotalTranscriptDTplot.out
    Untracked:  code/UTR2FASTA.py
    Untracked:  code/Upstream10Bases_general.py
    Untracked:  code/allPASSeq_df.sh
    Untracked:  code/apaQTLsnake.err
    Untracked:  code/apaQTLsnake.out
    Untracked:  code/apaQTLsnakePAS.err
    Untracked:  code/apaQTLsnakePAS.out
    Untracked:  code/apaQTLsnakePAShuman.err
    Untracked:  code/apaQTLsnakefiltPAS.err
    Untracked:  code/apaQTLsnakefiltPAS.out
    Untracked:  code/assignPeak2Intronicregion.err
    Untracked:  code/assignPeak2Intronicregion.out
    Untracked:  code/assignPeak2Intronicregion.sh
    Untracked:  code/bam2junc.err
    Untracked:  code/bam2junc.out
    Untracked:  code/bam2junc_remove.err
    Untracked:  code/bam2junc_remove.out
    Untracked:  code/bed215upbed.py
    Untracked:  code/bed2Bedbothstrand.py
    Untracked:  code/bed2SAF_gen.py
    Untracked:  code/bed2saf.py
    Untracked:  code/bg_to_cov.py
    Untracked:  code/buildIndecpantro5
    Untracked:  code/buildIndecpantro5.sh
    Untracked:  code/buildLeafviz.err
    Untracked:  code/buildLeafviz.out
    Untracked:  code/buildLeafviz.sh
    Untracked:  code/buildLeafviz_leadAnno.sh
    Untracked:  code/buildLeafviz_leafanno.err
    Untracked:  code/buildLeafviz_leafanno.out
    Untracked:  code/buildStarIndex.sh
    Untracked:  code/callPeaksYL.py
    Untracked:  code/chimpChromprder.sh
    Untracked:  code/chimpMultiCov.err
    Untracked:  code/chimpMultiCov.out
    Untracked:  code/chimpMultiCov.sh
    Untracked:  code/chimpMultiCov255.sh
    Untracked:  code/chimpMultiCovInclusive.err
    Untracked:  code/chimpMultiCovInclusive.out
    Untracked:  code/chimpMultiCovInclusive.sh
    Untracked:  code/chooseAnno2Bed.py
    Untracked:  code/chooseAnno2SAF.py
    Untracked:  code/chooseSignalSite.py
    Untracked:  code/chromOrder.err
    Untracked:  code/chromOrder.out
    Untracked:  code/classifyLeafviz.err
    Untracked:  code/classifyLeafviz.out
    Untracked:  code/cleanbed2saf.py
    Untracked:  code/cluster.json
    Untracked:  code/cluster2bed.py
    Untracked:  code/clusterLiftReverse.sh
    Untracked:  code/clusterLiftReverse_removebad.sh
    Untracked:  code/clusterLiftprimary.sh
    Untracked:  code/clusterLiftprimary_removebad.sh
    Untracked:  code/clusterPAS.json
    Untracked:  code/clusterfiltPAS.json
    Untracked:  code/comands2Mege.sh
    Untracked:  code/converBam2Junc.sh
    Untracked:  code/converBam2Junc_removeBad.sh
    Untracked:  code/convertNumeric.py
    Untracked:  code/environment.yaml
    Untracked:  code/extraSnakefiltpas
    Untracked:  code/extractPhaastConGeneral.py
    Untracked:  code/extractPhyloReg.py
    Untracked:  code/extractPhyloRegGene.py
    Untracked:  code/extractPhylopGeneral.py
    Untracked:  code/extractPhylopReg200down.py
    Untracked:  code/extractPhylopReg200up.py
    Untracked:  code/filter5perc.R
    Untracked:  code/filter5percPAS.py
    Untracked:  code/filter5percPheno.py
    Untracked:  code/filterBamforMP.pysam2_gen.py
    Untracked:  code/filterJuncChroms.err
    Untracked:  code/filterJuncChroms.out
    Untracked:  code/filterMissprimingInNuc10_gen.py
    Untracked:  code/filterNumChroms.py
    Untracked:  code/filterPASforMP.py
    Untracked:  code/filterPostLift.py
    Untracked:  code/filterPrimaryread.py
    Untracked:  code/filterSAFforMP_gen.py
    Untracked:  code/filterSecondaryread.py
    Untracked:  code/filterSortBedbyCleanedBed_gen.R
    Untracked:  code/filterpeaks.py
    Untracked:  code/fixExonFC.py
    Untracked:  code/fixFChead.py
    Untracked:  code/fixFChead_bothfrac.py
    Untracked:  code/fixFCheadforExp.py
    Untracked:  code/fixLeafCluster.py
    Untracked:  code/fixLiftedJunc.py
    Untracked:  code/fixUTRexonanno.py
    Untracked:  code/formathg38Anno.py
    Untracked:  code/generateStarIndex.err
    Untracked:  code/generateStarIndex.out
    Untracked:  code/generateStarIndexHuman.err
    Untracked:  code/generateStarIndexHuman.out
    Untracked:  code/getAlloverlap.py
    Untracked:  code/getRNAseqMapStats.sh
    Untracked:  code/hg19MapStats.err
    Untracked:  code/hg19MapStats.out
    Untracked:  code/hg19MapStats.sh
    Untracked:  code/humanChromorder.sh
    Untracked:  code/humanFiles
    Untracked:  code/humanMultiCov.err
    Untracked:  code/humanMultiCov.out
    Untracked:  code/humanMultiCov.sh
    Untracked:  code/humanMultiCov255.err
    Untracked:  code/humanMultiCov255.out
    Untracked:  code/humanMultiCov255.sh
    Untracked:  code/humanMultiCovInclusive.err
    Untracked:  code/humanMultiCovInclusive.out
    Untracked:  code/humanMultiCov_inclusive.sh
    Untracked:  code/infoContentSimpson.py
    Untracked:  code/intersectAnno.err
    Untracked:  code/intersectAnno.out
    Untracked:  code/intersectAnnoExt.err
    Untracked:  code/intersectAnnoExt.out
    Untracked:  code/intersectLiftedPAS.sh
    Untracked:  code/leafcutter_merge_regtools_redo.py
    Untracked:  code/liftJunctionFiles.sh
    Untracked:  code/liftPAS19to38.sh
    Untracked:  code/liftVCF.out
    Untracked:  code/liftVCF.sh
    Untracked:  code/liftoverPAShg19to38.err
    Untracked:  code/liftoverPAShg19to38.out
    Untracked:  code/lliftVCF.err
    Untracked:  code/log/
    Untracked:  code/make5percPeakbed.py
    Untracked:  code/makeDIC.err
    Untracked:  code/makeDIC.out
    Untracked:  code/makeFileID.py
    Untracked:  code/makeNuclearDapaplots.sh
    Untracked:  code/makeNuclearDapaplots_DF.sh
    Untracked:  code/makeNuclearPlots.err
    Untracked:  code/makeNuclearPlots.out
    Untracked:  code/makeNuclearPlotsDF.err
    Untracked:  code/makeNuclearPlotsDF.out
    Untracked:  code/makePheno.py
    Untracked:  code/makeSamplyGroupsChimp_TvN.py
    Untracked:  code/makeSamplyGroupsHuman_TvN.py
    Untracked:  code/makedICPlots_DF.sh
    Untracked:  code/mapRNAseqhg19.sh
    Untracked:  code/mapRNAseqhg19_newPipeline.sh
    Untracked:  code/maphg19.err
    Untracked:  code/maphg19.out
    Untracked:  code/maphg19.sh
    Untracked:  code/maphg19_new.err
    Untracked:  code/maphg19_new.out
    Untracked:  code/maphg19_sub.err
    Untracked:  code/maphg19_sub.out
    Untracked:  code/maphg19_subjunc.sh
    Untracked:  code/mediation_test.R
    Untracked:  code/merge.err
    Untracked:  code/mergeChimp3prime_inhg38.sh
    Untracked:  code/mergeChimpRNA.sh
    Untracked:  code/merge_leafcutter_clusters_redo.py
    Untracked:  code/mergeandBWRNAseq.sh
    Untracked:  code/mergeandsort_ChimpinHuman.err
    Untracked:  code/mergeandsort_ChimpinHuman.out
    Untracked:  code/mergeandsort_H3K9me3
    Untracked:  code/mergeandsort_h3k36me3
    Untracked:  code/mergeandsorth3k36me3.sh
    Untracked:  code/mergedBam2BW.sh
    Untracked:  code/mergedbam2bw.err
    Untracked:  code/mergedbam2bw.out
    Untracked:  code/mergedbamRNAand2bw.err
    Untracked:  code/mergedbamRNAand2bw.out
    Untracked:  code/nameClusters.py
    Untracked:  code/namePeaks.py
    Untracked:  code/negativeMediation_montecarlo.R
    Untracked:  code/negativeMediation_montecarloDF.R
    Untracked:  code/nuclearTranscriptDTplot.err
    Untracked:  code/nuclearTranscriptDTplot.out
    Untracked:  code/numMultimap.py
    Untracked:  code/overlapMMandOrthoexon.sh
    Untracked:  code/overlapPAS.err
    Untracked:  code/overlapPAS.out
    Untracked:  code/overlapPASandOrthoexon.sh
    Untracked:  code/overlapapaQTLPAS.sh
    Untracked:  code/overlapapaQTLPAS_extended.sh
    Untracked:  code/overlapapaQTLPAS_samples.sh
    Untracked:  code/parseHg38.py
    Untracked:  code/peak2PAS.py
    Untracked:  code/pheno2countonly.R
    Untracked:  code/postiveMediation_montecarlo.R
    Untracked:  code/postiveMediation_montecarlo_DF.R
    Untracked:  code/prepareAnnoLeafviz.err
    Untracked:  code/prepareAnnoLeafviz.out
    Untracked:  code/prepareCleanLiftedFC_5perc4LC.py
    Untracked:  code/prepareLeafvizAnno.sh
    Untracked:  code/preparePAS4lift.py
    Untracked:  code/prepare_phenotype_table.py
    Untracked:  code/primaryLift.err
    Untracked:  code/primaryLift.out
    Untracked:  code/primaryLift.sh
    Untracked:  code/processhg38exons.py
    Untracked:  code/quantJunc.sh
    Untracked:  code/quantJunc_TEST.sh
    Untracked:  code/quantJunc_removeBad.sh
    Untracked:  code/quantLiftedPAS.err
    Untracked:  code/quantLiftedPAS.out
    Untracked:  code/quantLiftedPAS.sh
    Untracked:  code/quantLiftedPASPrimary.err
    Untracked:  code/quantLiftedPASPrimary.out
    Untracked:  code/quantLiftedPASPrimary.sh
    Untracked:  code/quatJunc.err
    Untracked:  code/quatJunc.out
    Untracked:  code/recChimpback2Human.err
    Untracked:  code/recChimpback2Human.out
    Untracked:  code/recLiftchim2human.sh
    Untracked:  code/revLift.err
    Untracked:  code/revLift.out
    Untracked:  code/revLiftPAShg38to19.sh
    Untracked:  code/reverseLift.sh
    Untracked:  code/runCheckReverseLift.sh
    Untracked:  code/runChimpDiffIso.sh
    Untracked:  code/runChimpDiffIsoDF.sh
    Untracked:  code/runCountNucleotides.err
    Untracked:  code/runCountNucleotides.out
    Untracked:  code/runCountNucleotides.sh
    Untracked:  code/runCountNucleotidesPantro6.err
    Untracked:  code/runCountNucleotidesPantro6.out
    Untracked:  code/runCountNucleotides_pantro6.sh
    Untracked:  code/runFilterNumChroms.sh
    Untracked:  code/runHumanDiffIso.sh
    Untracked:  code/runHumanDiffIsoDF.sh
    Untracked:  code/runNewDom.sh
    Untracked:  code/runNuclearDiffIso_DF.sh
    Untracked:  code/runNuclearDifffIso.sh
    Untracked:  code/runTotalDiffIso.sh
    Untracked:  code/run_Chimpleafcutter_ds.err
    Untracked:  code/run_Chimpleafcutter_ds.out
    Untracked:  code/run_Chimpverifybam.err
    Untracked:  code/run_Chimpverifybam.out
    Untracked:  code/run_Humanleafcutter_dF.err
    Untracked:  code/run_Humanleafcutter_dF.out
    Untracked:  code/run_Humanleafcutter_ds.err
    Untracked:  code/run_Humanleafcutter_ds.out
    Untracked:  code/run_Nuclearleafcutter_ds.err
    Untracked:  code/run_Nuclearleafcutter_ds.out
    Untracked:  code/run_Nuclearleafcutter_dsDF.err
    Untracked:  code/run_Nuclearleafcutter_dsDF.out
    Untracked:  code/run_Totalleafcutter_ds.err
    Untracked:  code/run_Totalleafcutter_ds.out
    Untracked:  code/run_chimpverifybam.sh
    Untracked:  code/run_verifyBam.sh
    Untracked:  code/run_verifybam.err
    Untracked:  code/run_verifybam.out
    Untracked:  code/slurm-62824013.out
    Untracked:  code/slurm-62825841.out
    Untracked:  code/slurm-62826116.out
    Untracked:  code/slurm-64108209.out
    Untracked:  code/slurm-64108521.out
    Untracked:  code/slurm-64108557.out
    Untracked:  code/snakePASChimp.err
    Untracked:  code/snakePASChimp.out
    Untracked:  code/snakePAShuman.out
    Untracked:  code/snakemake.batch
    Untracked:  code/snakemakeChimp.err
    Untracked:  code/snakemakeChimp.out
    Untracked:  code/snakemakeHuman.err
    Untracked:  code/snakemakeHuman.out
    Untracked:  code/snakemakePAS.batch
    Untracked:  code/snakemakePASFiltChimp.err
    Untracked:  code/snakemakePASFiltChimp.out
    Untracked:  code/snakemakePASFiltHuman.err
    Untracked:  code/snakemakePASFiltHuman.out
    Untracked:  code/snakemakePAS_Human.batch
    Untracked:  code/snakemakePASchimp.batch
    Untracked:  code/snakemakePAShuman.batch
    Untracked:  code/snakemake_chimp.batch
    Untracked:  code/snakemake_human.batch
    Untracked:  code/snakemakefiltPAS.batch
    Untracked:  code/snakemakefiltPAS_chimp.sh
    Untracked:  code/snakemakefiltPAS_human.batch
    Untracked:  code/snakemakefiltPAS_human.sh
    Untracked:  code/spliceSite2Fasta.py
    Untracked:  code/submit-snakemake-chimp.sh
    Untracked:  code/submit-snakemake-human.sh
    Untracked:  code/submit-snakemakePAS-chimp.sh
    Untracked:  code/submit-snakemakePAS-human.sh
    Untracked:  code/submit-snakemakefiltPAS-chimp.sh
    Untracked:  code/submit-snakemakefiltPAS-human.sh
    Untracked:  code/subset_diffisopheno.py
    Untracked:  code/subset_diffisopheno_Chimp_tvN.py
    Untracked:  code/subset_diffisopheno_Chimp_tvN_DF.py
    Untracked:  code/subset_diffisopheno_Huma_tvN.py
    Untracked:  code/subset_diffisopheno_Huma_tvN_DF.py
    Untracked:  code/subset_diffisopheno_Nuclear_HvC.py
    Untracked:  code/subset_diffisopheno_Nuclear_HvC_DF.py
    Untracked:  code/subset_diffisopheno_Total_HvC.py
    Untracked:  code/test
    Untracked:  code/test.txt
    Untracked:  code/threeprimeOrthoFC.out
    Untracked:  code/threeprimeOrthoFC.sh
    Untracked:  code/threeprimeOrthoFCcd.err
    Untracked:  code/transcriptDTplotsNuclear.sh
    Untracked:  code/transcriptDTplotsTotal.sh
    Untracked:  code/verifyBam4973.sh
    Untracked:  code/verifyBam4973inHuman.sh
    Untracked:  code/verifybam4973.err
    Untracked:  code/verifybam4973.out
    Untracked:  code/verifybam4973HumanMap.err
    Untracked:  code/verifybam4973HumanMap.out
    Untracked:  code/wrap_Chimpverifybam.err
    Untracked:  code/wrap_Chimpverifybam.out
    Untracked:  code/wrap_chimpverifybam.sh
    Untracked:  code/wrap_verifyBam.sh
    Untracked:  code/wrap_verifybam.err
    Untracked:  code/wrap_verifybam.out
    Untracked:  code/writeMergecode.py
    Untracked:  data/._.DS_Store
    Untracked:  data/._HC_filenames.txt
    Untracked:  data/._HC_filenames.txt.sb-4426323c-IKIs0S
    Untracked:  data/._HC_filenames.xlsx
    Untracked:  data/._MapPantro6_meta.txt
    Untracked:  data/._MapPantro6_meta.txt.sb-a5794dd2-Cskmlm
    Untracked:  data/._MapPantro6_meta.xlsx
    Untracked:  data/._OppositeSpeciesMap.txt
    Untracked:  data/._OppositeSpeciesMap.txt.sb-a5794dd2-mayWJf
    Untracked:  data/._OppositeSpeciesMap.xlsx
    Untracked:  data/._RNASEQ_metadata.txt
    Untracked:  data/._RNASEQ_metadata.txt.sb-4426323c-TE4ns3
    Untracked:  data/._RNASEQ_metadata.txt.sb-51f67ae1-HXp7Gq
    Untracked:  data/._RNASEQ_metadata_2Removed.txt
    Untracked:  data/._RNASEQ_metadata_2Removed.txt.sb-4426323c-a4lBwx
    Untracked:  data/._RNASEQ_metadata_2Removed.xlsx
    Untracked:  data/._RNASEQ_metadata_stranded.txt
    Untracked:  data/._RNASEQ_metadata_stranded.txt.sb-a5794dd2-D659m2
    Untracked:  data/._RNASEQ_metadata_stranded.txt.sb-a5794dd2-ImNMoY
    Untracked:  data/._RNASEQ_metadata_stranded.txt.sb-e4bf31f0-ZGnGgl
    Untracked:  data/._RNASEQ_metadata_stranded.xlsx
    Untracked:  data/._TrialFiltersMeta.txt
    Untracked:  data/._TrialFiltersMeta.txt.sb-9845453e-R58Y0Q
    Untracked:  data/._metadata_HCpanel.txt
    Untracked:  data/._metadata_HCpanel.txt.sb-a3d92a2d-b9cYoF
    Untracked:  data/._metadata_HCpanel.txt.sb-a5794dd2-i594qs
    Untracked:  data/._metadata_HCpanel.txt.sb-f4823d1e-qihGek
    Untracked:  data/._metadata_HCpanel_frompantro5.xlsx
    Untracked:  data/._~$RNASEQ_metadata.xlsx
    Untracked:  data/._~$metadata_HCpanel.xlsx
    Untracked:  data/._.xlsx
    Untracked:  data/AREelements/
    Untracked:  data/BaseComp/
    Untracked:  data/CleanLiftedPeaks_FC_primary/
    Untracked:  data/CompapaQTLpas/
    Untracked:  data/DIC_Viz/
    Untracked:  data/DNDS/
    Untracked:  data/DTmatrix/
    Untracked:  data/DiffDomandDE_example/
    Untracked:  data/DiffExpression/
    Untracked:  data/DiffIso_Nuclear/
    Untracked:  data/DiffIso_Nuclear_DF/
    Untracked:  data/DiffIso_Total/
    Untracked:  data/DiffSplice/
    Untracked:  data/DiffSplice_liftedJunc/
    Untracked:  data/DiffSplice_removeBad/
    Untracked:  data/DistTwoDom/
    Untracked:  data/DomDefGreaterX/
    Untracked:  data/DomStructure_4/
    Untracked:  data/DominantPAS/
    Untracked:  data/DominantPAS_DF/
    Untracked:  data/DoubleFilterUsageNumeric/
    Untracked:  data/EvalPantro5/
    Untracked:  data/H3K36me3/
    Untracked:  data/HC_filenames.txt
    Untracked:  data/HC_filenames.xlsx
    Untracked:  data/HumanMolPheno/
    Untracked:  data/IndInfoContent/
    Untracked:  data/InfoContent/
    Untracked:  data/Khan_prot/
    Untracked:  data/Li_eqtls/
    Untracked:  data/MapPantro6_meta.txt
    Untracked:  data/MapPantro6_meta.xlsx
    Untracked:  data/MapStats/
    Untracked:  data/NormalizedClusters/
    Untracked:  data/NuclearHvC/
    Untracked:  data/NuclearHvC_DF/
    Untracked:  data/OppositeSpeciesMap.txt
    Untracked:  data/OppositeSpeciesMap.xlsx
    Untracked:  data/OrthoExonBed/
    Untracked:  data/OverlapBenchmark/
    Untracked:  data/OverlappingPAS/
    Untracked:  data/PAS/
    Untracked:  data/PAS_SAF/
    Untracked:  data/PAS_doubleFilter/
    Untracked:  data/PTM/
    Untracked:  data/Peaks_5perc/
    Untracked:  data/PhastCon/
    Untracked:  data/Pheno_5perc/
    Untracked:  data/Pheno_5perc_DF_nuclear/
    Untracked:  data/Pheno_5perc_nuclear/
    Untracked:  data/Pheno_5perc_nuclear_old/
    Untracked:  data/Pheno_5perc_total/
    Untracked:  data/PhyloP/
    Untracked:  data/Pol2Chip/
    Untracked:  data/QTLPASoverlap/
    Untracked:  data/RNASEQ_metadata.txt
    Untracked:  data/RNASEQ_metadata_2Removed.txt
    Untracked:  data/RNASEQ_metadata_2Removed.xlsx
    Untracked:  data/RNASEQ_metadata_stranded.txt
    Untracked:  data/RNASEQ_metadata_stranded.txt.sb-e4bf31f0-ZGnGgl/
    Untracked:  data/RNASEQ_metadata_stranded.xlsx
    Untracked:  data/SignalSites/
    Untracked:  data/SignalSites_doublefilter/
    Untracked:  data/SpliceSite/
    Untracked:  data/TestAnnoBiasOE/
    Untracked:  data/TestMM2/
    Untracked:  data/TestMM2_AS/
    Untracked:  data/TestMM2_PrimaryRead/
    Untracked:  data/TestMM2_SeondaryRead/
    Untracked:  data/TestMM2_mismatch/
    Untracked:  data/TestMM2_quality/
    Untracked:  data/TestWithinMergePAS/
    Untracked:  data/Test_FC_methods/
    Untracked:  data/Threeprime2Ortho/
    Untracked:  data/TotalFractionPAS/
    Untracked:  data/TotalHvC/
    Untracked:  data/TrialFiltersMeta.txt
    Untracked:  data/TwoBadSampleAnalysis/
    Untracked:  data/UrichElements/
    Untracked:  data/Wang_ribo/
    Untracked:  data/apaQTLGenes/
    Untracked:  data/bioGRID/
    Untracked:  data/chainFiles/
    Untracked:  data/cleanPeaks_anno/
    Untracked:  data/cleanPeaks_byspecies/
    Untracked:  data/cleanPeaks_lifted/
    Untracked:  data/files4viz_nuclear/
    Untracked:  data/files4viz_nuclear_DF/
    Untracked:  data/gviz/
    Untracked:  data/leafviz/
    Untracked:  data/liftover_files/
    Untracked:  data/mediation/
    Untracked:  data/mediation_DF/
    Untracked:  data/metadata_HCpanel.txt
    Untracked:  data/metadata_HCpanel.xlsx
    Untracked:  data/metadata_HCpanel_extra.txt
    Untracked:  data/metadata_HCpanel_frompantro5.txt
    Untracked:  data/metadata_HCpanel_frompantro5.xlsx
    Untracked:  data/miRNA/
    Untracked:  data/multimap/
    Untracked:  data/orthoUTR/
    Untracked:  data/paiDecay/
    Untracked:  data/primaryLift/
    Untracked:  data/reverseLift/
    Untracked:  data/testQuant/
    Untracked:  data/utrDB/
    Untracked:  data/~$RNASEQ_metadata.xlsx
    Untracked:  data/~$metadata_HCpanel.xlsx
    Untracked:  data/.xlsx
    Untracked:  output/._.DS_Store
    Untracked:  output/DEandTEeffectsize
    Untracked:  output/DEandTEeffectsize.pdf
    Untracked:  output/DEeffectsize
    Untracked:  output/DEeffectsize.pdf
    Untracked:  output/PropSamesdom
    Untracked:  output/PropSamesdom.pdf
    Untracked:  output/TEeffectsize
    Untracked:  output/TEeffectsize.pdf
    Untracked:  output/Total_DEeffectsize
    Untracked:  output/Total_DEeffectsize.pdf
    Untracked:  output/Total_DEeffectsizeNotJusttop.pdf
    Untracked:  output/Total_TEeffectsize
    Untracked:  output/Total_TEeffectsize.pdf
    Untracked:  output/Ubiqplot
    Untracked:  output/dAPAandDomEnrich.png
    Untracked:  output/dEandDomEnrich.png
    Untracked:  output/dediffdom.pdf
    Untracked:  output/dpnotDE
    Untracked:  output/dtPlots/
    Untracked:  output/exandte
    Untracked:  output/piecharts
    Untracked:  output/piecharts.pdf
    Untracked:  output/simpson.pdf
    Untracked:  output/whichSiteplot.pdf
    Untracked:  projectNotes.Rmd
    Untracked:  proteinModelSet.Rmd

Unstaged changes:
    Modified:   analysis/DeandNumPAS.Rmd
    Modified:   analysis/DirSelectionKhan.Rmd
    Modified:   analysis/EffectSizeRelationshipFixDir.Rmd
    Modified:   analysis/ExploredAPA.Rmd
    Modified:   analysis/MMExpreiment.Rmd
    Modified:   analysis/OppositeMap.Rmd
    Modified:   analysis/PTM_analysis.Rmd
    Modified:   analysis/TotalDomStructure.Rmd
    Modified:   analysis/TotalVNuclearBothSpecies.Rmd
    Modified:   analysis/annotationInfo.Rmd
    Modified:   analysis/changeMisprimcut.Rmd
    Modified:   analysis/comp2apaQTLPAS.Rmd
    Modified:   analysis/correlationPhenos.Rmd
    Modified:   analysis/dInforContent.Rmd
    Modified:   analysis/diffExpression.Rmd
    Modified:   analysis/establishCutoffs.Rmd
    Modified:   analysis/incorporateQTLsAncestral.Rmd
    Modified:   analysis/investigatePantro5.Rmd
    Modified:   analysis/mRNADecay.Rmd
    Modified:   analysis/miRNAanalysis.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/phastCon.Rmd
    Modified:   analysis/pol2.Rmd
    Modified:   analysis/speciesSpecific.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File	Version	Author	Date	Message
Rmd	1cc5ab7	brimittleman	2020-05-28	add total diff

In this analysis I will call site level dAPA in the total fraction the compare the effect size relationships with the de data.

I ran the original total human v chimp data in https://brimittleman.github.io/Comparative_APA/Total_HvC.html

library(qvalue)
library(tidyverse)

── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──

✔ ggplot2 3.1.1       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.3.1  
✔ readr   1.3.1       ✔ forcats 0.3.0

── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

library(ggpubr)

Loading required package: magrittr


Attaching package: 'magrittr'

The following object is masked from 'package:purrr':

    set_names

The following object is masked from 'package:tidyr':

    extract

library(cowplot)


Attaching package: 'cowplot'

The following object is masked from 'package:ggpubr':

    get_legend

The following object is masked from 'package:ggplot2':

    ggsave

Meta=read.table("../data/PAS_doubleFilter/PAS_5perc_either_HumanCoord_BothUsage_meta_doubleFilter.txt", header = T, stringsAsFactors = F)  %>% dplyr::select(PAS, chr, start,end, loc)
DiffIso= read.table("../data/DiffIso_Total/AllPAS_withGeneSig.txt", header = T,stringsAsFactors = F) %>% inner_join(Meta, by=c("chr", 'start','end')) %>% filter(loc %in% c("intron","utr3"))

DiffIsoTop=DiffIso %>% mutate(AvgUsageBoth=(Human+Chimp)/2) %>% group_by(gene) %>% arrange(p.adjust,desc(AvgUsageBoth)) %>% slice(1) %>% ungroup()

DiffIsoTop %>% group_by(loc) %>% summarise(n())

# A tibble: 2 x 2
  loc    `n()`
  <chr>  <int>
1 intron   751
2 utr3    7310

Expression:

nameID=read.table("../../genome_anotation_data/ensemble_to_genename.txt",sep="\t", header = T, stringsAsFactors = F) %>% dplyr::select(Gene_stable_ID, Gene.name)

DE=read.table("../data/DiffExpression/DEtested_allres.txt",stringsAsFactors = F,header = F, col.names = c("Gene_stable_ID" ,"logFC" ,"AveExpr" , "t" ,  "P.Value" ,  "adj.P.Val", "B"  )) %>% inner_join(nameID,by="Gene_stable_ID") %>% dplyr::rename('gene'=Gene.name) %>% dplyr::select(-Gene_stable_ID) %>% mutate(CorrectedlogFC=-1*logFC)

Translation:

Ribo=read.table("../data/Wang_ribo/Additionaltable5_translationComparisons.txt",header = T, stringsAsFactors = F) %>% rename("Gene_stable_ID"= ENSG) %>% inner_join(nameID,by="Gene_stable_ID") %>% dplyr::select(Gene.name, HvC.beta, HvC.pvalue, HvC.FDR) %>% rename("gene"=Gene.name)

DeandAPA= DiffIsoTop %>% inner_join(DE, by="gene")

nrow(DeandAPA)

[1] 7366

DeandAPA %>% group_by(loc) %>% summarise(n())

# A tibble: 2 x 2
  loc    `n()`
  <chr>  <int>
1 intron   413
2 utr3    6953

DE_all=ggplot(DeandAPA,aes(y=deltaPAU, x=CorrectedlogFC)) + geom_point(alpha=.3) + geom_smooth(method="lm") + labs(title="Total APA v DE", x="DE log effect size", y="Difference in PAS Usage") + scale_color_brewer(palette = "Set1",name="", labels=c("Intronic", "3' UTR"))+ stat_cor(label.x = -8,label.y = -1) +theme_classic(base_size = 12)

DE_all

DE_split=ggplot(DeandAPA,aes(y=deltaPAU, x=CorrectedlogFC, col=loc)) + geom_point(alpha=.3) + geom_smooth(aes(col=loc),method="lm") + labs(title="Total APA v DE", x="DE log effect size", y="Difference in PAS Usage") + scale_color_brewer(palette = "Set1",name="", labels=c("Intronic", "3' UTR"))+ stat_cor(aes(col=loc),label.x = c(-8,-1),label.y = -1) +theme_classic(base_size = 12)

DE_split

DeandAPASig= DeandAPA %>% filter(SigPAU2=="Yes", adj.P.Val<=0.05)

nrow(DeandAPASig)

[1] 352

DeandAPASig %>% group_by(loc) %>% summarise(n())

# A tibble: 2 x 2
  loc    `n()`
  <chr>  <int>
1 intron    24
2 utr3     328

DE_sig_all=ggplot(DeandAPASig,aes(y=deltaPAU, x=CorrectedlogFC)) + geom_point(alpha=.3) + geom_smooth(method="lm") + labs(title="TotalSignificant differences in Total APA and expression", x="DE log effect size", y="Difference in PAS Usage") + scale_color_brewer(palette = "Set1",name="", labels=c("Intronic", "3' UTR"))+ stat_cor(label.x = -8,label.y = -1) +theme_classic(base_size = 12)

DE_sig_all

DE_sig_split=ggplot(DeandAPASig,aes(y=deltaPAU, x=CorrectedlogFC, col=loc)) + geom_point(alpha=.3) + geom_smooth(aes(col=loc),method="lm") + labs(title="Significant differences in Total APA and expression", x="DE log effect size", y="Difference in PAS Usage") + scale_color_brewer(palette = "Set1",name="", labels=c("Intronic", "3' UTR"))+ stat_cor(aes(col=loc),label.x = c(-8,-1),label.y = -1) +theme_classic(base_size = 12)

DE_sig_split

plot_grid(DE_all, DE_split,DE_sig_all,DE_sig_split)

RiboandAPA= DiffIsoTop %>% inner_join(Ribo, by="gene")

nrow(RiboandAPA)

[1] 6389

TE_all=ggplot(RiboandAPA,aes(y=deltaPAU, x=HvC.beta)) + geom_point(alpha=.3) + geom_smooth(method="lm") + labs(title="Total APA v TE", x="TE effect size", y="Difference in PAS Usage") + scale_color_brewer(palette = "Set1",name="", labels=c("Intronic", "3' UTR"))+ stat_cor(label.x = -8,label.y = -1) +theme_classic(base_size = 12)

TE_all

TE_split=ggplot(RiboandAPA,aes(y=deltaPAU, x=HvC.beta, col=loc)) + geom_point(alpha=.3) + geom_smooth(aes(col=loc),method="lm") + labs(title="Total APA v TE", x="TE effect size", y="Difference in PAS Usage") + scale_color_brewer(palette = "Set1",name="", labels=c("Intronic", "3' UTR"))+ stat_cor(aes(col=loc),label.x = c(-8,1),label.y = -1) +theme_classic(base_size = 12)

TE_split

RiboandAPASig= RiboandAPA %>% filter(SigPAU2=="Yes", HvC.FDR<=0.05)

nrow(RiboandAPASig)

[1] 163

TE_sig_all=ggplot(RiboandAPASig,aes(y=deltaPAU, x=HvC.beta)) + geom_point(alpha=.3) + geom_smooth(method="lm") + labs(title="Significant differences in Total APA and translation", x="TE effect size", y="Difference in PAS Usage") + scale_color_brewer(palette = "Set1",name="", labels=c("Intronic", "3' UTR"))+ stat_cor(label.x = -8,label.y = -1) +theme_classic(base_size = 12)

TE_sig_all

TE_sig_split=ggplot(RiboandAPASig,aes(y=deltaPAU, x=HvC.beta, col=loc)) + geom_point(alpha=.3) + geom_smooth(aes(col=loc),method="lm") + labs(title="Significant differences in Total APA and translation", x="TE effect size", y="Difference in PAS Usage") + scale_color_brewer(palette = "Set1",name="", labels=c("Intronic", "3' UTR"))+ stat_cor(aes(col=loc),label.x = c(-8,1),label.y = -1) +theme_classic(base_size = 12)

TE_sig_split

plot_grid(TE_all, TE_split,TE_sig_all,TE_sig_split)

Make the DE plot without the top used. Count all

DeandAPAAll= DiffIso %>% inner_join(DE, by="gene")

DeandAPAAll %>% group_by(loc) %>% summarise(n())

# A tibble: 2 x 2
  loc    `n()`
  <chr>  <int>
1 intron 11217
2 utr3   15661

DeandAPAAllsig= DeandAPAAll%>% filter(SigPAU2=="Yes", adj.P.Val<=0.05)

denotsubsig=ggplot(DeandAPAAllsig,aes(y=deltaPAU, x=CorrectedlogFC, col=loc)) + geom_point(alpha=.3) + geom_smooth(aes(col=loc),method="lm") + labs(title="Significant differences in Total APA and expression \n(not just top used)", x="DE log effect size", y="Difference in PAS Usage") + scale_color_brewer(palette = "Set1",name="", labels=c("Intronic", "3' UTR"))+ stat_cor(aes(col=loc),label.x = c(-8,-1),label.y = -1) +theme_classic(base_size = 12)


denotsub=ggplot(DeandAPAAll,aes(y=deltaPAU, x=CorrectedlogFC, col=loc)) + geom_point(alpha=.3) + geom_smooth(aes(col=loc),method="lm") + labs(title=" Total APA and expression\n (not just top used)", x="DE log effect size", y="Difference in PAS Usage") + scale_color_brewer(palette = "Set1",name="", labels=c("Intronic", "3' UTR"))+ stat_cor(aes(col=loc),label.x = c(-8,-1),label.y = -1) +theme_classic(base_size = 12)

plot_grid(denotsub,denotsubsig)

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] cowplot_0.9.4   ggpubr_0.2      magrittr_1.5    forcats_0.3.0  
 [5] stringr_1.3.1   dplyr_0.8.0.1   purrr_0.3.2     readr_1.3.1    
 [9] tidyr_0.8.3     tibble_2.1.1    ggplot2_3.1.1   tidyverse_1.2.1
[13] qvalue_2.14.0  

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5   reshape2_1.4.3     splines_3.5.1     
 [4] haven_1.1.2        lattice_0.20-38    colorspace_1.3-2  
 [7] generics_0.0.2     htmltools_0.3.6    yaml_2.2.0        
[10] utf8_1.1.4         rlang_0.4.0        later_0.7.5       
[13] pillar_1.3.1       withr_2.1.2        glue_1.3.0        
[16] RColorBrewer_1.1-2 modelr_0.1.2       readxl_1.1.0      
[19] plyr_1.8.4         munsell_0.5.0      gtable_0.2.0      
[22] workflowr_1.6.0    cellranger_1.1.0   rvest_0.3.2       
[25] evaluate_0.12      labeling_0.3       knitr_1.20        
[28] httpuv_1.4.5       fansi_0.4.0        broom_0.5.1       
[31] Rcpp_1.0.4.6       promises_1.0.1     scales_1.0.0      
[34] backports_1.1.2    jsonlite_1.6       fs_1.3.1          
[37] hms_0.4.2          digest_0.6.18      stringi_1.2.4     
[40] grid_3.5.1         rprojroot_1.3-2    cli_1.1.0         
[43] tools_3.5.1        lazyeval_0.2.1     crayon_1.3.4      
[46] whisker_0.3-2      pkgconfig_2.0.2    xml2_1.2.0        
[49] lubridate_1.7.4    assertthat_0.2.0   rmarkdown_1.10    
[52] httr_1.3.1         rstudioapi_0.10    R6_2.3.0          
[55] nlme_3.1-137       git2r_0.26.1       compiler_3.5.1

APA and expression effect size relationship in total

Briana Mittleman

5/28/2020