Redo Expression Effect Size plot- Chimp Negative on both scales

Last updated: 2020-05-21

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: 89a7189

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/liftoverPAShg19to38.err
    Untracked:  code/liftoverPAShg19to38.out
    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/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/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/DEeffectsize
    Untracked:  output/TEeffectsize
    Untracked:  output/dAPAandDomEnrich.png
    Untracked:  output/dEandDomEnrich.png
    Untracked:  output/dpnotDE
    Untracked:  output/dtPlots/
    Untracked:  output/exandte
    Untracked:  output/whichSiteplot.pdf
    Untracked:  projectNotes.Rmd
    Untracked:  proteinModelSet.Rmd

Unstaged changes:
    Modified:   analysis/DeandNumPAS.Rmd
    Modified:   analysis/DiffTop2SecondDom.Rmd
    Modified:   analysis/DirSelectionKhan.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/investigatePantro5.Rmd
    Modified:   analysis/mRNADecay.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/phastCon.Rmd
    Modified:   analysis/pol2.Rmd
    Modified:   analysis/signalsites_doublefilter.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	89a7189	brimittleman	2020-05-21	add fix effect dir and intronic plots

Untill now I have been plotting effect size correlations between human and chimp for expression, translation, and APA using inconsitent directions.

I will flip the expression effect sizes to match the apa delta PAU.

Chimp will be negative Human will be postivie

library(ggpubr)

Loading required package: ggplot2

#stat cor is pearson 
library(qvalue)
library(tidyverse)

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

✔ tibble  2.1.3     ✔ purrr   0.3.2
✔ tidyr   1.1.0     ✔ dplyr   0.8.3
✔ readr   1.3.1     ✔ stringr 1.4.0
✔ tibble  2.1.3     ✔ forcats 0.4.0

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

library("viridis")

Loading required package: viridisLite

library(cowplot)


********************************************************

Note: As of version 1.0.0, cowplot does not change the

  default ggplot2 theme anymore. To recover the previous

  behavior, execute:
  theme_set(theme_cowplot())

********************************************************


Attaching package: 'cowplot'

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

    get_legend

Load data

APA data:

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_Nuclear_DF/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()

I will use the top used PAS for all plots (colored and not colored). This way there is no bias in the set.
###Expression data

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 data:

In this analysis - was already up regulated in chimp

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)

Plot data

APA and expression

All data:

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

nrow(DeandAPA)

[1] 7391

DE_all=ggplot(DeandAPA,aes(y=deltaPAU, x=CorrectedlogFC)) + geom_point(alpha=.3) + geom_smooth(method="lm") + labs(title="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

Seperate by size:

DE_split=ggplot(DeandAPA,aes(y=deltaPAU, x=CorrectedlogFC, col=loc)) + geom_point(alpha=.3) + geom_smooth(aes(col=loc),method="lm") + labs(title="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(-8,0),label.y = -1) +theme_classic(base_size = 12)

DE_split

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

# A tibble: 2 x 2
  loc    `n()`
  <chr>  <int>
1 intron  1313
2 utr3    6078

Subset to significant in both:

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

nrow(DeandAPASig)

[1] 408

DE_sig_all=ggplot(DeandAPASig,aes(y=deltaPAU, x=CorrectedlogFC)) + geom_point(alpha=.3) + geom_smooth(method="lm") + labs(title="Significant differences in 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

Seperate by size:

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 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(-8,0),label.y = -1) +theme_classic(base_size = 12)

DE_sig_split

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

# A tibble: 2 x 2
  loc    `n()`
  <chr>  <int>
1 intron    65
2 utr3     343

plot together:

plot_grid(DE_all, DE_split,DE_sig_all,DE_sig_split)

APA and translation

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

nrow(RiboandAPA)

[1] 6407

TE_all=ggplot(RiboandAPA,aes(y=deltaPAU, x=HvC.beta)) + geom_point(alpha=.3) + geom_smooth(method="lm") + labs(title="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

Seperate by size:

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="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(-8,0),label.y = -1) +theme_classic(base_size = 12)

TE_split

Number of intronic and 3’ UTR

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

# A tibble: 2 x 2
  loc    `n()`
  <chr>  <int>
1 intron  1138
2 utr3    5269

Subset to significant in both:

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

nrow(RiboandAPASig)

[1] 214

TE_sig_all=ggplot(RiboandAPASig,aes(y=deltaPAU, x=HvC.beta)) + geom_point(alpha=.3) + geom_smooth(method="lm") + labs(title="Significant differences in 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

Seperate by size:

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 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(-8,0),label.y = -1) +theme_classic(base_size = 12)

TE_sig_split

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

# A tibble: 2 x 2
  loc    `n()`
  <chr>  <int>
1 intron    37
2 utr3     177

plot together:

plot_grid(TE_all, TE_split,TE_sig_all,TE_sig_split)

plot DE and TE

plot_grid(DE_sig_all,TE_sig_all,DE_sig_split, TE_sig_split)

sessionInfo()

R version 3.6.1 (2019-07-05)
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_1.0.0     viridis_0.5.1     viridisLite_0.3.0
 [4] forcats_0.4.0     stringr_1.4.0     dplyr_0.8.3      
 [7] purrr_0.3.2       readr_1.3.1       tidyr_1.1.0      
[10] tibble_2.1.3      tidyverse_1.2.1   qvalue_2.16.0    
[13] ggpubr_0.3.0      ggplot2_3.2.1    

loaded via a namespace (and not attached):
 [1] httr_1.4.0         jsonlite_1.6       splines_3.6.1     
 [4] carData_3.0-2      modelr_0.1.4       assertthat_0.2.1  
 [7] cellranger_1.1.0   yaml_2.2.0         pillar_1.4.2      
[10] backports_1.1.4    lattice_0.20-38    glue_1.3.1        
[13] digest_0.6.20      RColorBrewer_1.1-2 promises_1.0.1    
[16] ggsignif_0.5.0     rvest_0.3.4        colorspace_1.4-1  
[19] htmltools_0.3.6    httpuv_1.5.1       plyr_1.8.4        
[22] pkgconfig_2.0.2    broom_0.5.2        haven_2.1.1       
[25] scales_1.1.0       whisker_0.3-2      openxlsx_4.1.0.1  
[28] later_0.8.0        rio_0.5.16         git2r_0.26.1      
[31] generics_0.0.2     farver_2.0.1       car_3.0-5         
[34] withr_2.1.2        lazyeval_0.2.2     cli_1.1.0         
[37] magrittr_1.5       crayon_1.3.4       readxl_1.3.1      
[40] evaluate_0.14      fs_1.3.1           fansi_0.4.0       
[43] nlme_3.1-140       rstatix_0.5.0      xml2_1.2.0        
[46] foreign_0.8-71     tools_3.6.1        data.table_1.12.8 
[49] hms_0.5.0          lifecycle_0.1.0    munsell_0.5.0     
[52] zip_2.0.3          compiler_3.6.1     rlang_0.4.6       
[55] grid_3.6.1         rstudioapi_0.10    labeling_0.3      
[58] rmarkdown_1.13     gtable_0.3.0       abind_1.4-5       
[61] curl_3.3           reshape2_1.4.3     R6_2.4.0          
[64] gridExtra_2.3      lubridate_1.7.4    knitr_1.23        
[67] utf8_1.1.4         workflowr_1.6.0    rprojroot_1.3-2   
[70] stringi_1.4.3      Rcpp_1.0.3         vctrs_0.3.0       
[73] tidyselect_1.1.0   xfun_0.8

Redo Expression Effect Size plot- Chimp Negative on both scales

Briana Mittleman

5/21/2020

Load data

APA data:

Translation data:

Plot data

APA and expression

APA and translation

plot DE and TE