Last updated: 2019-06-20

Checks: 6 0

Knit directory: apaQTL/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.3.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


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.

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.

The command set.seed(20190411) 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.

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

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

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:    data/.DS_Store
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  .Rprofile
    Untracked:  ._.DS_Store
    Untracked:  .gitignore
    Untracked:  _workflowr.yml
    Untracked:  analysis/._PASdescriptiveplots.Rmd
    Untracked:  analysis/._cuttoffPercUsage.Rmd
    Untracked:  analysis/QTLexampleplots.Rmd
    Untracked:  analysis/cuttoffPercUsage.Rmd
    Untracked:  analysis/eQTLoverlap.Rmd
    Untracked:  analysis/mergeRNA.Rmd
    Untracked:  analysis/oldstuffNotNeeded.Rmd
    Untracked:  apaQTL.Rproj
    Untracked:  code/.NascentRNAdtPlotFirstintronicPAS.sh.swp
    Untracked:  code/._ApaQTL_nominalNonnorm.sh
    Untracked:  code/._BothFracDTPlotGeneRegions_normalized.sh
    Untracked:  code/._EandPqtls.sh
    Untracked:  code/._FC_NucintornUpandDown.sh
    Untracked:  code/._FC_UTR.sh
    Untracked:  code/._FC_intornUpandDownsteamPAS.sh
    Untracked:  code/._FC_newPeaks_olddata.sh
    Untracked:  code/._HMMpermuteTotal.py
    Untracked:  code/._HmmPermute.py
    Untracked:  code/._LC_samplegroups.py
    Untracked:  code/._NascentRNAdtPlot.sh
    Untracked:  code/._NascentRNAdtPlot3UTRPAS.sh
    Untracked:  code/._NascentRNAdtPlotExcludeFirstintronicPAS.sh
    Untracked:  code/._NascentRNAdtPlotNucPAS.sh
    Untracked:  code/._NascentRNAdtPlotTotPAS.sh
    Untracked:  code/._NascentRNAdtPlotintronicPAS.sh
    Untracked:  code/._NascnetRNAdtPlotPAS.sh
    Untracked:  code/._NetSeq_fourthintronDT.sh
    Untracked:  code/._QTL2bed.py
    Untracked:  code/._QTL2bed_withstrand.py
    Untracked:  code/._RNAbam2bw.sh
    Untracked:  code/._SnakefilePAS
    Untracked:  code/._SnakefilefiltPAS
    Untracked:  code/._TESplots100bp.sh
    Untracked:  code/._TESplots150bp.sh
    Untracked:  code/._TESplots200bp.sh
    Untracked:  code/._Untitled
    Untracked:  code/._ZipandTabPheno.sh
    Untracked:  code/._aAPAqtl_nominal39ind.sh
    Untracked:  code/._apaQTLCorrectPvalMakeQQ.R
    Untracked:  code/._apaQTL_Nominal.sh
    Untracked:  code/._apaQTL_permuted.sh
    Untracked:  code/._assignNucIntonpeak2intronlocs.sh
    Untracked:  code/._assignTotIntronpeak2intronlocs.sh
    Untracked:  code/._bam2BW_5primemost.sh
    Untracked:  code/._bed2saf.py
    Untracked:  code/._bothFracDTplot1stintron.sh
    Untracked:  code/._bothFracDTplot4thintron.sh
    Untracked:  code/._bothFrac_FC.sh
    Untracked:  code/._callPeaksYL.py
    Untracked:  code/._changenomQTLres2geneName.py
    Untracked:  code/._chooseAnno2SAF.py
    Untracked:  code/._chooseSignalSite
    Untracked:  code/._chooseSignalSite.py
    Untracked:  code/._cluster.json
    Untracked:  code/._clusterPAS.json
    Untracked:  code/._clusterfiltPAS.json
    Untracked:  code/._codingdms2bed.py
    Untracked:  code/._config.yaml
    Untracked:  code/._config2.yaml
    Untracked:  code/._configOLD.yaml
    Untracked:  code/._convertNominal2SNPLOC.py
    Untracked:  code/._convertNumeric.py
    Untracked:  code/._correctNomeqtl.R
    Untracked:  code/._dag.pdf
    Untracked:  code/._eQTLgenestestedapa.py
    Untracked:  code/._encodeRNADTplots.sh
    Untracked:  code/._extractGenotypes.py
    Untracked:  code/._extractseqfromqtlfastq.py
    Untracked:  code/._fc2leafphen.py
    Untracked:  code/._filter5perc.R
    Untracked:  code/._filter5percPheno.py
    Untracked:  code/._filterpeaks.py
    Untracked:  code/._finalPASbed2SAF.py
    Untracked:  code/._fix4su304corr.py
    Untracked:  code/._fix4su604corr.py
    Untracked:  code/._fix4sukalisto.py
    Untracked:  code/._fixExandUnexeQTL
    Untracked:  code/._fixExandUnexeQTL.py
    Untracked:  code/._fixFChead.py
    Untracked:  code/._fixFChead_bothfrac.py
    Untracked:  code/._fixH3k12ac.py
    Untracked:  code/._fixRNAhead4corr.py
    Untracked:  code/._fixRNAkalisto.py
    Untracked:  code/._fixgroupedtranscript.py
    Untracked:  code/._fixhead_netseqfc.py
    Untracked:  code/._getAPAfromanyeQTL.py
    Untracked:  code/._getApapval4eqtl.py
    Untracked:  code/._getApapval4eqtl_unexp.py
    Untracked:  code/._getDownstreamIntronNuclear.py
    Untracked:  code/._getIntronDownstreamPAS.py
    Untracked:  code/._getIntronUpstreamPAS.py
    Untracked:  code/._getQTLalleles.py
    Untracked:  code/._getQTLfastq.sh
    Untracked:  code/._getUpstreamIntronNuclear.py
    Untracked:  code/._grouptranscripts.py
    Untracked:  code/._keep5perMAF.py
    Untracked:  code/._keepSNP_vcf.sh
    Untracked:  code/._make5percPeakbed.py
    Untracked:  code/._makeFileID.py
    Untracked:  code/._makePheno.py
    Untracked:  code/._makeSAFbothfrac5perc.py
    Untracked:  code/._makeSNP2rsidfile.py
    Untracked:  code/._makeeQTLempirical_unexp.py
    Untracked:  code/._makeeQTLempiricaldist.py
    Untracked:  code/._makegencondeTSSfile.py
    Untracked:  code/._mergRNABam.sh
    Untracked:  code/._mergeAllBam.sh
    Untracked:  code/._mergeBW_norm.sh
    Untracked:  code/._mergeBamNascent.sh
    Untracked:  code/._mergeByFracBam.sh
    Untracked:  code/._mergePeaks.sh
    Untracked:  code/._mnase1stintron.sh
    Untracked:  code/._mnaseDT_fourthintron.sh
    Untracked:  code/._namePeaks.py
    Untracked:  code/._netseqDTplot1stIntron.sh
    Untracked:  code/._netseqFC.sh
    Untracked:  code/._peak2PAS.py
    Untracked:  code/._peakFC.sh
    Untracked:  code/._pheno2countonly.R
    Untracked:  code/._phenoQTLfromlist.py
    Untracked:  code/._processYRIgen.py
    Untracked:  code/._qtlRegionseq.sh
    Untracked:  code/._qtlsPvalOppFrac.py
    Untracked:  code/._quantassign2parsedpeak.py
    Untracked:  code/._removeXfromHmm.py
    Untracked:  code/._removeloc_pheno.py
    Untracked:  code/._runCorrectNomEqtl.sh
    Untracked:  code/._runHMMpermuteAPAqtls.sh
    Untracked:  code/._runHMMpermuteeQTLS.sh
    Untracked:  code/._runMakeEmpiricaleQTL_unexp.sh
    Untracked:  code/._runMakeeQTLempirical.sh
    Untracked:  code/._run_getApaPval4eqtl.sh
    Untracked:  code/._run_getapafromeQTL.py
    Untracked:  code/._run_getapafromeQTL.sh
    Untracked:  code/._run_getapapval4eqtl_unexp.sh
    Untracked:  code/._run_leafcutterDiffIso.sh
    Untracked:  code/._run_sepUsagephen.sh
    Untracked:  code/._run_sepgenobychrom.sh
    Untracked:  code/._selectNominalPvalues.py
    Untracked:  code/._sepUsagePhen.py
    Untracked:  code/._sepgenobychrom.py
    Untracked:  code/._snakemakePAS.batch
    Untracked:  code/._snakemakefiltPAS.batch
    Untracked:  code/._sortindexRNAbam.sh
    Untracked:  code/._submit-snakemakePAS.sh
    Untracked:  code/._submit-snakemakefiltPAS.sh
    Untracked:  code/._subsetAPAnotEorPgene.py
    Untracked:  code/._subsetApanoteGene.py
    Untracked:  code/._subsetUnexplainedeQTLs.py
    Untracked:  code/._subset_diffisopheno.py
    Untracked:  code/._subsetpermAPAwithGenelist.py
    Untracked:  code/._subtrachfiveprimeUTR.sh
    Untracked:  code/._subtractExons.sh
    Untracked:  code/._subtractfiveprimeUTR.sh
    Untracked:  code/._tabixSNPS.sh
    Untracked:  code/._utrdms2saf.py
    Untracked:  code/.snakemake/
    Untracked:  code/APAqtl_nominal.err
    Untracked:  code/APAqtl_nominal.out
    Untracked:  code/APAqtl_nominal_39.err
    Untracked:  code/APAqtl_nominal_39.out
    Untracked:  code/APAqtl_nominal_nonNorm.err
    Untracked:  code/APAqtl_nominal_nonNorm.out
    Untracked:  code/APAqtl_permuted.err
    Untracked:  code/APAqtl_permuted.out
    Untracked:  code/ApaQTL_nominalNonnorm.sh
    Untracked:  code/BothFracDTPlot1stintron.err
    Untracked:  code/BothFracDTPlot1stintron.out
    Untracked:  code/BothFracDTPlot4stintron.err
    Untracked:  code/BothFracDTPlot4stintron.out
    Untracked:  code/BothFracDTPlotGeneRegions.err
    Untracked:  code/BothFracDTPlotGeneRegions.out
    Untracked:  code/BothFracDTPlotGeneRegions_norm.err
    Untracked:  code/BothFracDTPlotGeneRegions_norm.out
    Untracked:  code/BothFracDTPlotGeneRegions_normalized.sh
    Untracked:  code/DistPAS2Sig.py
    Untracked:  code/EandPqtl.err
    Untracked:  code/EandPqtl.out
    Untracked:  code/EandPqtls.sh
    Untracked:  code/EncodeRNADTPlotGeneRegions.err
    Untracked:  code/EncodeRNADTPlotGeneRegions.out
    Untracked:  code/FC_NucintornUpandDown.sh
    Untracked:  code/FC_NucintronPASupandDown.err
    Untracked:  code/FC_NucintronPASupandDown.out
    Untracked:  code/FC_UTR.err
    Untracked:  code/FC_UTR.out
    Untracked:  code/FC_UTR.sh
    Untracked:  code/FC_intornUpandDownsteamPAS.sh
    Untracked:  code/FC_intronPASupandDown.err
    Untracked:  code/FC_intronPASupandDown.out
    Untracked:  code/FC_newPAS_olddata.err
    Untracked:  code/FC_newPAS_olddata.out
    Untracked:  code/FC_newPeaks_olddata.sh
    Untracked:  code/HMMpermuteTotal.py
    Untracked:  code/HmmPermute.p
    Untracked:  code/HmmPermute.py
    Untracked:  code/LC_samplegroups.py
    Untracked:  code/NascentDTPlotGeneRegions.err
    Untracked:  code/NascentDTPlotGeneRegions.out
    Untracked:  code/NascentDTPlotPAS.err
    Untracked:  code/NascentDTPlotPAS.out
    Untracked:  code/NascentDTPlotPAS_3utr.err
    Untracked:  code/NascentDTPlotPAS_3utr.out
    Untracked:  code/NascentDTPlotPAS_firstintron.err
    Untracked:  code/NascentDTPlotPAS_firstintron.out
    Untracked:  code/NascentDTPlotPAS_intron.err
    Untracked:  code/NascentDTPlotPAS_intron.out
    Untracked:  code/NascentDTPlotPAS_nuc.err
    Untracked:  code/NascentDTPlotPAS_nuc.out
    Untracked:  code/NascentDTPlotPAS_tot.err
    Untracked:  code/NascentDTPlotPAS_tot.out
    Untracked:  code/NascentRNAdtPlot.sh
    Untracked:  code/NascentRNAdtPlot3UTRPAS.sh
    Untracked:  code/NascentRNAdtPlotExcludeFirstintronicPAS.sh
    Untracked:  code/NascentRNAdtPlotFirstintronicPAS.sh
    Untracked:  code/NascentRNAdtPlotNucPAS.sh
    Untracked:  code/NascentRNAdtPlotTotPAS.sh
    Untracked:  code/NascentRNAdtPlotintronicPAS.sh
    Untracked:  code/NascnetRNAdtPlotPAS.sh
    Untracked:  code/NetSeq_fourthintronDT.sh
    Untracked:  code/Nuclear_example.err
    Untracked:  code/Nuclear_example.out
    Untracked:  code/QTL2bed.py
    Untracked:  code/QTL2bed_withstrand.py
    Untracked:  code/README.md
    Untracked:  code/RNABam2BW.err
    Untracked:  code/RNABam2BW.out
    Untracked:  code/RNAbam2bw.sh
    Untracked:  code/Rplots.pdf
    Untracked:  code/Script4NuclearQTLexamples.sh
    Untracked:  code/Script4TotalQTLexamples.sh
    Untracked:  code/TESplots100bp.err
    Untracked:  code/TESplots100bp.out
    Untracked:  code/TESplots100bp.sh
    Untracked:  code/TESplots150bp.err
    Untracked:  code/TESplots150bp.out
    Untracked:  code/TESplots150bp.sh
    Untracked:  code/TESplots200bp.err
    Untracked:  code/TESplots200bp.out
    Untracked:  code/TESplots200bp.sh
    Untracked:  code/Total_example.err
    Untracked:  code/Total_example.out
    Untracked:  code/Untitled
    Untracked:  code/Upstream100Bases_general.py
    Untracked:  code/ZipandTabPheno.sh
    Untracked:  code/aAPAqtl_nominal39ind.sh
    Untracked:  code/apaQTLCorrectPvalMakeQQ_4pc.R
    Untracked:  code/apaQTL_Nominal_4pc.sh
    Untracked:  code/apaQTL_permuted.4pc.sh
    Untracked:  code/apafacetboxplots.R
    Untracked:  code/apaqtlfacetboxplots.R
    Untracked:  code/assignNucIntonpeak2intronlocs.sh
    Untracked:  code/assignPeak2Intronicregion.err
    Untracked:  code/assignPeak2Intronicregion.out
    Untracked:  code/assignTotIntronpeak2intronlocs.sh
    Untracked:  code/assigntotPeak2Intronicregion.err
    Untracked:  code/assigntotPeak2Intronicregion.out
    Untracked:  code/bam2BW_5primemost.sh
    Untracked:  code/bam2bw.err
    Untracked:  code/bam2bw.out
    Untracked:  code/bam2bw_5primemost.err
    Untracked:  code/bam2bw_5primemost.out
    Untracked:  code/bothFracDTplot1stintron.sh
    Untracked:  code/bothFracDTplot4thintron.sh
    Untracked:  code/bothFrac_FC.err
    Untracked:  code/bothFrac_FC.out
    Untracked:  code/bothFrac_FC.sh
    Untracked:  code/changenomQTLres2geneName.py
    Untracked:  code/codingdms2bed.py
    Untracked:  code/convertNominal2SNPLOC.py
    Untracked:  code/correctNomeqtl.R
    Untracked:  code/dag.pdf
    Untracked:  code/dagPAS.pdf
    Untracked:  code/dagfiltPAS.pdf
    Untracked:  code/eQTLgenestestedapa.py
    Untracked:  code/encodeRNADTplots.sh
    Untracked:  code/extractGenotypes.py
    Untracked:  code/extractseqfromqtlfastq.py
    Untracked:  code/fc2leafphen.py
    Untracked:  code/finalPASbed2SAF.py
    Untracked:  code/findbuginpeaks.R
    Untracked:  code/fix4su304corr.py
    Untracked:  code/fix4su604corr.py
    Untracked:  code/fix4sukalisto.py
    Untracked:  code/fixExandUnexeQTL
    Untracked:  code/fixExandUnexeQTL.py
    Untracked:  code/fixFChead_bothfrac.py
    Untracked:  code/fixFChead_summary.py
    Untracked:  code/fixH3k12ac.py
    Untracked:  code/fixRNAhead4corr.py
    Untracked:  code/fixRNAkalisto.py
    Untracked:  code/fixgroupedtranscript.py
    Untracked:  code/fixhead_netseqfc.py
    Untracked:  code/genotypesYRI.gen.proc.keep.vcf.log
    Untracked:  code/genotypesYRI.gen.proc.keep.vcf.recode.vcf
    Untracked:  code/get100upPAS.py
    Untracked:  code/getAPAfromanyeQTL.py
    Untracked:  code/getApapval4eqtl.py
    Untracked:  code/getApapval4eqtl_unexp.py
    Untracked:  code/getDownstreamIntronNuclear.py
    Untracked:  code/getIntronDownstreamPAS.py
    Untracked:  code/getIntronUpstreamPAS.py
    Untracked:  code/getQTLalleles.py
    Untracked:  code/getQTLfastq.sh
    Untracked:  code/getSeq100up.sh
    Untracked:  code/getUpstreamIntronNuclear.py
    Untracked:  code/getseq100up.err
    Untracked:  code/getseq100up.out
    Untracked:  code/grouptranscripts.err
    Untracked:  code/grouptranscripts.out
    Untracked:  code/grouptranscripts.py
    Untracked:  code/keep5perMAF.py
    Untracked:  code/keepSNP_vcf.sh
    Untracked:  code/log/
    Untracked:  code/makeSAFbothfrac5perc.py
    Untracked:  code/makeSNP2rsidfile.py
    Untracked:  code/makeeQTLempirical_unexp.py
    Untracked:  code/makeeQTLempiricaldist.py
    Untracked:  code/makegencondeTSSfile.py
    Untracked:  code/mergRNABam.sh
    Untracked:  code/mergeBW_norm.sh
    Untracked:  code/mergeBWnorm.err
    Untracked:  code/mergeBWnorm.out
    Untracked:  code/mergeBamNacent.err
    Untracked:  code/mergeBamNacent.out
    Untracked:  code/mergeBamNascent.sh
    Untracked:  code/mergeRNAbam.err
    Untracked:  code/mergeRNAbam.out
    Untracked:  code/mnase1stintron.sh
    Untracked:  code/mnaseDTPlot1stintron.err
    Untracked:  code/mnaseDTPlot1stintron.out
    Untracked:  code/mnaseDTPlot4thintron.err
    Untracked:  code/mnaseDTPlot4thintron.out
    Untracked:  code/mnaseDT_fourthintron.sh
    Untracked:  code/netDTPlot4thintron.out
    Untracked:  code/netseqDTplot1stIntron.sh
    Untracked:  code/netseqFC.err
    Untracked:  code/netseqFC.out
    Untracked:  code/netseqFC.sh
    Untracked:  code/neyDTPlot4thintron.err
    Untracked:  code/phenoQTLfromlist.py
    Untracked:  code/processYRIgen.py
    Untracked:  code/qtlFacetBoxplots.err
    Untracked:  code/qtlFacetBoxplots.out
    Untracked:  code/qtlRegionseq.sh
    Untracked:  code/qtlsPvalOppFrac.py
    Untracked:  code/removeXfromHmm.py
    Untracked:  code/removeloc_pheno.py
    Untracked:  code/runCorrectNomEqtl.sh
    Untracked:  code/runCorrectNomeqtl.err
    Untracked:  code/runCorrectNomeqtl.out
    Untracked:  code/runHMMpermute.err
    Untracked:  code/runHMMpermute.out
    Untracked:  code/runHMMpermuteAPAqtls.sh
    Untracked:  code/runHMMpermuteeQTLS.sh
    Untracked:  code/runHMMpermuteeQTLs.err
    Untracked:  code/runHMMpermuteeQTLs.out
    Untracked:  code/runMakeEmpiricaleQTL_unexp.sh
    Untracked:  code/runMakeEmpiricaleQTLs.err
    Untracked:  code/runMakeEmpiricaleQTLs.out
    Untracked:  code/runMakeEmpiricaleQTLsunex.err
    Untracked:  code/runMakeEmpiricaleQTLsunex.out
    Untracked:  code/runMakeeQTLempirical.sh
    Untracked:  code/run_DistPAS2Sig.err
    Untracked:  code/run_DistPAS2Sig.out
    Untracked:  code/run_distPAS2Sig.sh
    Untracked:  code/run_getAPAfromanyeQTL.err
    Untracked:  code/run_getAPAfromanyeQTL.out
    Untracked:  code/run_getApaPval4eQTLs.err
    Untracked:  code/run_getApaPval4eQTLs.out
    Untracked:  code/run_getApaPval4eQTLsunexplained.err
    Untracked:  code/run_getApaPval4eQTLsunexplained.out
    Untracked:  code/run_getApaPval4eqtl.sh
    Untracked:  code/run_getapafromeQTL.sh
    Untracked:  code/run_getapapval4eqtl_unexp.sh
    Untracked:  code/run_leafcutterDiffIso.sh
    Untracked:  code/run_leafcutter_ds.err
    Untracked:  code/run_leafcutter_ds.out
    Untracked:  code/run_qtlFacetBoxplots.sh
    Untracked:  code/run_sepUsagephen.sh
    Untracked:  code/run_sepgenobychrom.err
    Untracked:  code/run_sepgenobychrom.out
    Untracked:  code/run_sepgenobychrom.sh
    Untracked:  code/run_sepusage.err
    Untracked:  code/run_sepusage.out
    Untracked:  code/selectNominalPvalues.py
    Untracked:  code/sepUsagePhen.py
    Untracked:  code/sepgenobychrom.py
    Untracked:  code/seqQTLfastq.err
    Untracked:  code/seqQTLfastq.out
    Untracked:  code/seqQTLregion.err
    Untracked:  code/seqQTLregion.out
    Untracked:  code/snakePASlog.out
    Untracked:  code/snakefiltPASlog.out
    Untracked:  code/sortindexRNABam.err
    Untracked:  code/sortindexRNABam.out
    Untracked:  code/sortindexRNAbam.sh
    Untracked:  code/subsetAPAnotEorPgene.py
    Untracked:  code/subsetApanoteGene.py
    Untracked:  code/subsetUnexplainedeQTLs.py
    Untracked:  code/subset_diffisopheno.py
    Untracked:  code/subsetpermAPAwithGenelist.py
    Untracked:  code/subtract5UTR.err
    Untracked:  code/subtract5UTR.out
    Untracked:  code/subtractExons.err
    Untracked:  code/subtractExons.out
    Untracked:  code/subtractExons.sh
    Untracked:  code/subtractfiveprimeUTR.sh
    Untracked:  code/tabixSNPS.sh
    Untracked:  code/tabixSNPs.err
    Untracked:  code/tabixSNPs.out
    Untracked:  code/transcriptdm2bed.py
    Untracked:  code/utrdms2saf.py
    Untracked:  code/vcf_keepsnps.err
    Untracked:  code/vcf_keepsnps.out
    Untracked:  code/writeExampleQTLcode.py
    Untracked:  code/zipandtabPhen.err
    Untracked:  code/zipandtabPhen.out
    Untracked:  data/._.DS_Store
    Untracked:  data/ApaByEgene/
    Untracked:  data/ApaByPgene/
    Untracked:  data/Battle_pQTL/
    Untracked:  data/CompareOldandNew/
    Untracked:  data/DTmatrix/
    Untracked:  data/DiffIso/
    Untracked:  data/EncodeRNA/
    Untracked:  data/ExampleQTLPlots/
    Untracked:  data/GeuvadisRNA/
    Untracked:  data/HMMqtls/
    Untracked:  data/Li_eQTLs/
    Untracked:  data/NascentRNA/
    Untracked:  data/NucSpeceQTLeffect/
    Untracked:  data/PAS/
    Untracked:  data/QTLGenotypes/
    Untracked:  data/QTLoverlap/
    Untracked:  data/QTLoverlap_nonNorm/
    Untracked:  data/README.md
    Untracked:  data/RNAseq/
    Untracked:  data/Reads2UTR/
    Untracked:  data/SignalSiteFiles/
    Untracked:  data/ThirtyNineIndQtl_nominal/
    Untracked:  data/apaQTLNominal/
    Untracked:  data/apaQTLNominal_4pc/
    Untracked:  data/apaQTLPermuted/
    Untracked:  data/apaQTLPermuted_4pc/
    Untracked:  data/apaQTLs/
    Untracked:  data/assignedPeaks/
    Untracked:  data/bam/
    Untracked:  data/bam_clean/
    Untracked:  data/bam_waspfilt/
    Untracked:  data/bed_10up/
    Untracked:  data/bed_clean/
    Untracked:  data/bed_clean_sort/
    Untracked:  data/bed_waspfilter/
    Untracked:  data/bedsort_waspfilter/
    Untracked:  data/bothFrac_FC/
    Untracked:  data/bw_norm/
    Untracked:  data/eQTLs/
    Untracked:  data/exampleQTLs/
    Untracked:  data/fastq/
    Untracked:  data/filterPeaks/
    Untracked:  data/fourSU/
    Untracked:  data/h3k27ac/
    Untracked:  data/highdiffsiggenes.txt
    Untracked:  data/inclusivePeaks/
    Untracked:  data/inclusivePeaks_FC/
    Untracked:  data/intronRNAratio/
    Untracked:  data/intron_analysis/
    Untracked:  data/mergedBG/
    Untracked:  data/mergedBW_byfrac/
    Untracked:  data/mergedBW_norm/
    Untracked:  data/mergedBam/
    Untracked:  data/mergedbyFracBam/
    Untracked:  data/molPhenos/
    Untracked:  data/molQTLs/
    Untracked:  data/motifdistrupt/
    Untracked:  data/netseq/
    Untracked:  data/nonNorm_pheno/
    Untracked:  data/nuc_10up/
    Untracked:  data/nuc_10upclean/
    Untracked:  data/overlapeQTL_try2/
    Untracked:  data/overlapeQTLs/
    Untracked:  data/peakCoverage/
    Untracked:  data/peaks_5perc/
    Untracked:  data/phenotype/
    Untracked:  data/phenotype_5perc/
    Untracked:  data/sigDiffGenes.txt
    Untracked:  data/sort/
    Untracked:  data/sort_clean/
    Untracked:  data/sort_waspfilter/
    Untracked:  nohup.out
    Untracked:  output/._.DS_Store
    Untracked:  output/._meanCorrelationPhenotypes.svg
    Untracked:  output/dtPlots/
    Untracked:  output/fastqc/
    Untracked:  output/meanCorrelationPhenotypes.svg

Unstaged changes:
    Modified:   analysis/Readdistagainstfeatures.Rmd
    Modified:   analysis/molQTL.Rmd
    Modified:   analysis/nascentRNA.Rmd
    Modified:   analysis/overlapapaqtlsandeqtls.Rmd
    Modified:   analysis/signalsiteanalysis.Rmd
    Modified:   code/BothFracDTPlotGeneRegions.sh
    Modified:   code/Snakefile
    Deleted:    code/Upstream10Bases_general.py
    Modified:   code/apaQTLCorrectPvalMakeQQ.R
    Modified:   code/apaQTL_Nominal.sh
    Modified:   code/apaQTL_permuted.sh
    Modified:   code/apaQTLsnake.err
    Modified:   code/bam2bw.sh
    Modified:   code/bed2saf.py
    Modified:   code/cluster.json
    Modified:   code/clusterfiltPAS.json
    Modified:   code/config.yaml
    Modified:   code/environment.yaml
    Modified:   code/makePheno.py
    Deleted:    code/test.txt

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 b2def08 brimittleman 2019-06-20 first intron in sites with ss
html 5a02775 brimittleman 2019-06-18 Build site.
Rmd 078b340 brimittleman 2019-06-18 add first intron length
html b3328b6 brimittleman 2019-06-18 Build site.
Rmd 01bc8aa brimittleman 2019-06-18 add verify first inton res

In the previous analysis I saw that most of my intronic pas are in the first intron and skew toward the beginning of long introns. I will further explore this result here.

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(cowplot)

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

    ggsave
library(workflowr)
This is workflowr version 1.3.0
Run ?workflowr for help getting started

Nuclear

These are the nuclear intronic PAS

pas2intron=read.table("../data/intron_analysis/IntronPeaksontoIntrons.bed",col.names = c("intronCHR", "intronStart", "intronEnd", "gene", "score", "strand", "peakCHR", "peakStart", "peakEnd", "PeakID", "meanUsage", "peakStrand"),stringsAsFactors = F) %>% mutate(PASloc=ifelse(strand=="+", peakEnd, peakStart)) %>% dplyr::select(intronStart, intronEnd, gene, strand, PeakID, PASloc ,meanUsage) %>% mutate(intronLength=intronEnd-intronStart , distance2PAS= ifelse(strand=="+", PASloc-intronStart, intronEnd-PASloc), propIntron=distance2PAS/intronLength) %>% mutate(LengthCat=ifelse(intronLength<=3929, "first", ifelse(intronLength>3929 &intronLength<=9220, "second", ifelse(intronLength>9220 &intronLength<=24094, "third", "fourth"))))

pas2intron$LengthCat <- factor(pas2intron$LengthCat, levels=c("first", "second", "third", "fourth"))

Beginning of introns

I want to plot the absolute distance rather than the standardized distance to the 5’ ss.

ggplot(pas2intron,aes(x=distance2PAS, fill=LengthCat)) + geom_histogram(bins=100)  + facet_grid(~LengthCat) + xlim(0,5000)
Warning: Removed 6143 rows containing non-finite values (stat_bin).
Warning: Removed 8 rows containing missing values (geom_bar).

Version Author Date
b3328b6 brimittleman 2019-06-18
ggplot(pas2intron,aes(x=distance2PAS, fill=LengthCat))  + facet_grid(~LengthCat) + xlim(0,5000) +  stat_ecdf(aes(col=LengthCat)) 
Warning: Removed 6143 rows containing non-finite values (stat_ecdf).

Version Author Date
b3328b6 brimittleman 2019-06-18

First intron

This is not the correct analysis. I need to actually look at which intron from all of them.

this is the file I created to get the introns. I need to remove genes with only 1 introm.

introns=read.table("/project2/gilad/briana/apaQTL/data/intron_analysis/transcriptsMinusExons.sort.bed",stringsAsFactors = F, col.names = c("chrom", "intronStart", "intronEnd", "gene", "score", "strand")) %>% group_by(gene)  %>% filter(!grepl("hap",chrom)) %>% mutate(Intronid=ifelse(strand=="+",  1:n(),n():1), nintron=n()) %>% filter(nintron>2)

Join with PAS:

pas2intron_intron=pas2intron %>% inner_join(introns, by=c("intronStart","intronEnd","gene", "strand" ))
pas2intron_intron$Intronid=as.factor(pas2intron_intron$Intronid)


write.table(pas2intron_intron, "../data/intron_analysis/NuclearIntronPASwithWhichintron.txt", col.names = T, row.names = F, quote = F, sep="\t")
ggplot(pas2intron_intron,aes(x=Intronid)) +  geom_bar(stat="count") + labs(title="intron ID for nuclear intronic pas", x="intron ID")

Version Author Date
b3328b6 brimittleman 2019-06-18
summary(pas2intron_intron$Intronid)
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15 
3147 2111 1585 1278  896  725  633  503  432  384  287  238  188  178  145 
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30 
 119  113  106   83   71   56   63   48   58   40   36   31   18   14    9 
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45 
  11   12   13    6    3    6    5   10    7   11    9    8    5    9    6 
  46   47   48   49   50   51   52   53   55   57   58   59   60   64   66 
   2    3    1    1    6    4    7    4    1    3    6    3    1    1    5 
  67   68   69   70   72   73   74   76   77   79   85   88   89   90   94 
   4    4    5    1    3    2    1    1    2    1    1    3    2    1    2 
  96  160  165 
   2    1    2 

I want to see if the usage is the same over this:

pas2intron_intron_usagecat= pas2intron_intron %>% mutate(UsageCat=ifelse(meanUsage<=.1, "<.1", ifelse(meanUsage>.1 &meanUsage<=.2, "<.2", ifelse(meanUsage>.2 &meanUsage<=.3, "<.3", ">.3"))))
pas2intron_intron_usagecat$Intronid=as.numeric(as.character(pas2intron_intron_usagecat$Intronid))
ggplot(pas2intron_intron_usagecat,aes(x=Intronid, fill=UsageCat)) +  geom_bar(stat="count") + labs(title="intron ID for nuclear intronic pas", x="intron ID") + facet_grid(~UsageCat)+ xlim(0,10)
Warning: Removed 2108 rows containing non-finite values (stat_count).
Warning: Removed 4 rows containing missing values (geom_bar).

Version Author Date
b3328b6 brimittleman 2019-06-18

Maybe by the number of introns?

summary(pas2intron_intron_usagecat$nintron)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   3.00    6.00   11.00   14.41   18.00  171.00 
pas2intron_intron_usagecat_introncat= pas2intron_intron_usagecat %>% mutate(IntronCat=ifelse(nintron<=6, "first (<6)", ifelse(nintron>6 &nintron<=11, "second (6-11)", ifelse(nintron>11 &nintron<=18, "third (11-18)", "fourth (>18)"))))

pas2intron_intron_usagecat_introncat$IntronCat <- factor(pas2intron_intron_usagecat_introncat$IntronCat, levels=c("first (<6)", "second (6-11)", "third (11-18)", "fourth (>18)"))
ggplot(pas2intron_intron_usagecat_introncat,aes(x=Intronid, fill=IntronCat)) +  geom_bar(stat="count") + labs(title="intron ID for nuclear intronic pas", x="intron ID") + facet_grid(~IntronCat) + xlim(0,10)
Warning: Removed 2108 rows containing non-finite values (stat_count).
Warning: Removed 3 rows containing missing values (geom_bar).

Version Author Date
b3328b6 brimittleman 2019-06-18
nuclear_cdf=ggplot(pas2intron_intron_usagecat_introncat,aes(x=Intronid, fill=IntronCat)) +  stat_ecdf(aes(col=IntronCat)) + labs(title="intron ID for Nuclear intronic pas", x="intron ID") + xlim(0,10)+ geom_vline(xintercept = 2) 

Total

First intron

pas2intronTot=read.table("../data/intron_analysis/TotalIntronPeaksontoIntrons.bed",col.names = c("intronCHR", "intronStart", "intronEnd", "gene", "score", "strand", "peakCHR", "peakStart", "peakEnd", "PeakID", "meanUsage", "peakStrand"),stringsAsFactors = F) %>% mutate(PASloc=ifelse(strand=="+", peakEnd, peakStart)) %>% dplyr::select(intronStart, intronEnd, gene, strand, PeakID, PASloc ,meanUsage) %>% mutate(intronLength=intronEnd-intronStart , distance2PAS= ifelse(strand=="+", PASloc-intronStart, intronEnd-PASloc), propIntron=distance2PAS/intronLength) %>%  mutate(LengthCat=ifelse(intronLength<=3785, "first", ifelse(intronLength>3785 &intronLength<=8872, "second", ifelse(intronLength>8872 &intronLength<=22928, "third", "fourth"))))

pas2intronTot$LengthCat <- factor(pas2intronTot$LengthCat, levels=c("first", "second", "third", "fourth"))
pas2intronTot_intron=pas2intronTot %>% inner_join(introns, by=c("intronStart","intronEnd","gene", "strand" ))

write.table(pas2intronTot_intron, "../data/intron_analysis/TotalIntronPASwithWhichintron.txt", col.names = T, row.names = F, quote = F, sep="\t")
summary(pas2intronTot_intron$nintron)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   3.00    6.00   11.00   14.62   18.00  171.00 
pas2intronTot_intron_usagecat_introncat= pas2intronTot_intron %>% mutate(IntronCat=ifelse(nintron<=6, "first (<6)", ifelse(nintron>6 &nintron<=11, "second (6-11)", ifelse(nintron>11 &nintron<=18, "third (11-18)", "fourth (>18)"))))

ggplot(pas2intronTot_intron_usagecat_introncat,aes(x=Intronid, fill=IntronCat)) +  geom_bar(stat="count") + labs(title="intron ID for Total intronic pas", x="intron ID") + facet_grid(~IntronCat) + xlim(0,10)
Warning: Removed 1327 rows containing non-finite values (stat_count).
Warning: Removed 3 rows containing missing values (geom_bar).

Version Author Date
b3328b6 brimittleman 2019-06-18
totalcdf=ggplot(pas2intronTot_intron_usagecat_introncat,aes(x=Intronid, fill=IntronCat)) +  stat_ecdf(aes(col=IntronCat)) + labs(title="intron ID for Total intronic pas", x="intron ID") + xlim(0,10) + geom_vline(xintercept = 2) 

Both fracitons

Plot both:

pas2intronTot_intron_usagecat_introncat_frac=pas2intronTot_intron_usagecat_introncat %>% mutate(fraction="Total") %>% select(Intronid,IntronCat,fraction)

pas2intron_intron_usagecat_introncat_frac=pas2intron_intron_usagecat_introncat%>% mutate(fraction="Nuclear") %>% select(Intronid,IntronCat,fraction)

intronidboth=bind_rows(pas2intronTot_intron_usagecat_introncat_frac,pas2intron_intron_usagecat_introncat_frac)
Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector
ggplot(intronidboth,aes(x=Intronid)) +  stat_ecdf(aes(col=fraction)) + labs(title="intron ID for intronic pas", x="intron ID") + xlim(0,10) + facet_grid(~IntronCat)
Warning: Removed 3435 rows containing non-finite values (stat_ecdf).

Version Author Date
b3328b6 brimittleman 2019-06-18
plot_grid(nuclear_cdf,totalcdf)
Warning: Removed 2108 rows containing non-finite values (stat_ecdf).
Warning: Removed 1327 rows containing non-finite values (stat_ecdf).

Version Author Date
b3328b6 brimittleman 2019-06-18

Usage in both fractions.

TotalIntronicUsage=pas2intronTot_intron_usagecat_introncat %>% mutate(fraction="Total") %>% select(meanUsage,fraction)

NuclearIntronicUsage=pas2intron_intron_usagecat_introncat%>% mutate(fraction="Nuclear") %>% select(meanUsage,fraction)

bothIntronicUsage=bind_rows(TotalIntronicUsage,NuclearIntronicUsage)
ggplot(bothIntronicUsage, aes(x=meanUsage))  +  stat_ecdf(aes(col=fraction)) 

Version Author Date
b3328b6 brimittleman 2019-06-18

Final plot:
first intron (conditioned on the intron being > 2KB) shows no signal (plotting the first 2kb only)

firstintron_nuclear=pas2intron_intron_usagecat_introncat %>% filter(Intronid==1,intronLength>2000) 

firstintron_total=pas2intronTot_intron_usagecat_introncat %>% filter(Intronid==1,intronLength>2000) 
ggplot(firstintron_nuclear,aes(x=distance2PAS, fill=LengthCat)) + geom_histogram(bins=50) +xlim(0,2000) + facet_grid(~LengthCat)+ labs(title="Nuclear intronic PAS in first intron (3025)")
Warning: Removed 2280 rows containing non-finite values (stat_bin).
Warning: Removed 8 rows containing missing values (geom_bar).

Version Author Date
5a02775 brimittleman 2019-06-18
ggplot(firstintron_total,aes(x=distance2PAS, fill=LengthCat)) + geom_histogram(bins=50) +xlim(0,2000) + facet_grid(~LengthCat) + labs(title="Total intronic PAS in first intron (1804)")
Warning: Removed 1277 rows containing non-finite values (stat_bin).
Warning: Removed 8 rows containing missing values (geom_bar).

Version Author Date
5a02775 brimittleman 2019-06-18

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] workflowr_1.3.0 cowplot_0.9.4   forcats_0.3.0   stringr_1.3.1  
 [5] dplyr_0.8.0.1   purrr_0.3.2     readr_1.3.1     tidyr_0.8.3    
 [9] tibble_2.1.1    ggplot2_3.1.1   tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       cellranger_1.1.0 pillar_1.3.1     compiler_3.5.1  
 [5] git2r_0.25.2     plyr_1.8.4       tools_3.5.1      digest_0.6.18   
 [9] lubridate_1.7.4  jsonlite_1.6     evaluate_0.12    nlme_3.1-137    
[13] gtable_0.2.0     lattice_0.20-38  pkgconfig_2.0.2  rlang_0.3.1     
[17] cli_1.0.1        rstudioapi_0.10  yaml_2.2.0       haven_1.1.2     
[21] withr_2.1.2      xml2_1.2.0       httr_1.3.1       knitr_1.20      
[25] hms_0.4.2        generics_0.0.2   fs_1.2.6         rprojroot_1.3-2 
[29] grid_3.5.1       tidyselect_0.2.5 glue_1.3.0       R6_2.3.0        
[33] readxl_1.1.0     rmarkdown_1.10   reshape2_1.4.3   modelr_0.1.2    
[37] magrittr_1.5     whisker_0.3-2    backports_1.1.2  scales_1.0.0    
[41] htmltools_0.3.6  rvest_0.3.2      assertthat_0.2.0 colorspace_1.3-2
[45] labeling_0.3     stringi_1.2.4    lazyeval_0.2.1   munsell_0.5.0   
[49] broom_0.5.1      crayon_1.3.4