Last updated: 2019-06-07

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.

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(20190411)

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.

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.

Repository version: 32091ee

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:    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/cuttoffPercUsage.Rmd
    Untracked:  analysis/eQTLoverlap.Rmd
    Untracked:  analysis/intonRNAratio.Rmd
    Untracked:  apaQTL.Rproj
    Untracked:  code/.NascentRNAdtPlotFirstintronicPAS.sh.swp
    Untracked:  code/._ApaQTL_nominalNonnorm.sh
    Untracked:  code/._BothFracDTPlotGeneRegions_normalized.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/._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/._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/._convertNumeric.py
    Untracked:  code/._correctNomeqtl.R
    Untracked:  code/._dag.pdf
    Untracked:  code/._eQTLgenestestedapa.py
    Untracked:  code/._encodeRNADTplots.sh
    Untracked:  code/._extractGenotypes.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/._getIntronDownstreamPAS.py
    Untracked:  code/._getIntronUpstreamPAS.py
    Untracked:  code/._grouptranscripts.py
    Untracked:  code/._make5percPeakbed.py
    Untracked:  code/._makeFileID.py
    Untracked:  code/._makePheno.py
    Untracked:  code/._makeSAFbothfrac5perc.py
    Untracked:  code/._makeeQTLempirical_unexp.py
    Untracked:  code/._makeeQTLempiricaldist.py
    Untracked:  code/._makegencondeTSSfile.py
    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/._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_getapapval4eqtl_unexp.sh
    Untracked:  code/._run_leafcutterDiffIso.sh
    Untracked:  code/._run_sepUsagephen.sh
    Untracked:  code/._selectNominalPvalues.py
    Untracked:  code/._sepUsagePhen.py
    Untracked:  code/._snakemakePAS.batch
    Untracked:  code/._snakemakefiltPAS.batch
    Untracked:  code/._submit-snakemakePAS.sh
    Untracked:  code/._submit-snakemakefiltPAS.sh
    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/._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/EncodeRNADTPlotGeneRegions.err
    Untracked:  code/EncodeRNADTPlotGeneRegions.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/README.md
    Untracked:  code/Rplots.pdf
    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/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/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/codingdms2bed.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/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/get100upPAS.py
    Untracked:  code/getAPAfromanyeQTL.py
    Untracked:  code/getApapval4eqtl.py
    Untracked:  code/getApapval4eqtl_unexp.py
    Untracked:  code/getIntronDownstreamPAS.py
    Untracked:  code/getIntronUpstreamPAS.py
    Untracked:  code/getSeq100up.sh
    Untracked:  code/getseq100up.err
    Untracked:  code/getseq100up.out
    Untracked:  code/grouptranscripts.err
    Untracked:  code/grouptranscripts.out
    Untracked:  code/grouptranscripts.py
    Untracked:  code/log/
    Untracked:  code/makeSAFbothfrac5perc.py
    Untracked:  code/makeeQTLempirical_unexp.py
    Untracked:  code/makeeQTLempiricaldist.py
    Untracked:  code/makegencondeTSSfile.py
    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/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/qtlFacetBoxplots.err
    Untracked:  code/qtlFacetBoxplots.out
    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_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_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_sepusage.err
    Untracked:  code/run_sepusage.out
    Untracked:  code/selectNominalPvalues.py
    Untracked:  code/sepUsagePhen.py
    Untracked:  code/snakePASlog.out
    Untracked:  code/snakefiltPASlog.out
    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/transcriptdm2bed.py
    Untracked:  code/utrdms2saf.py
    Untracked:  code/zipandtabPhen.err
    Untracked:  code/zipandtabPhen.out
    Untracked:  data/ApaByEgene/
    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/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/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/DiffIsoAnalysis.Rmd
    Modified:   analysis/PASusageQC.Rmd
    Modified:   analysis/Readdistagainstfeatures.Rmd
    Modified:   analysis/choosePCs.Rmd
    Modified:   analysis/corrbetweenind.Rmd
    Modified:   analysis/exvunexpeQTL.Rmd
    Modified:   analysis/nascenttranscription.Rmd
    Modified:   analysis/nucintronicanalysis.Rmd
    Modified:   analysis/overlapapaqtlsandeqtls.Rmd
    Modified:   analysis/rerunQTL_changePC.Rmd
    Modified:   analysis/rna_netseq_h3k12ac.Rmd
    Modified:   code/BothFracDTPlotGeneRegions.sh
    Modified:   code/Snakefile
    Deleted:    code/Upstream10Bases_general.py
    Modified:   code/apaQTLCorrectPvalMakeQQ.R
    Modified:   code/apaQTL_permuted.sh
    Modified:   code/apaQTLsnake.err
    Modified:   code/bam2bw.sh
    Modified:   code/bed2saf.py
    Modified:   code/cluster.json
    Modified:   code/config.yaml
    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 32091ee brimittleman 2019-06-07 more prop explained to new analysis 
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(workflowr)
This is workflowr version 1.3.0
Run ?workflowr for help getting started

I need to fix the explained_FDR10.sort.txt and unexplained_FDR10.sort.txt files because right now this file has multiple genes per snp.

python fixExandUnexeQTL.py ../data/Li_eQTLs/explained_FDR10.sort.txt ../data/Li_eQTLs/explained_FDR10.sort_FIXED.txt
python fixExandUnexeQTL.py ../data/Li_eQTLs/unexplained_FDR10.sort.txt ../data/Li_eQTLs/unexplained_FDR10.sort_FIXED.txt

There are 1195 explained and 814 unexplained eQTLs. I will next look at each of these in my apadata.

mkdir ../data/overlapeQTL_try2
python getAPAfromanyeQTL.py ../data/apaQTLNominal_4pc/APApeak_Phenotype_GeneLocAnno.Total.5perc.fc.gz.qqnorm_AllChrom.txt ../data/Li_eQTLs/explained_FDR10.sort_FIXED.txt  ../data/overlapeQTL_try2/apaTotal_explainedQTLs.txt

python getAPAfromanyeQTL.py ../data/apaQTLNominal_4pc/APApeak_Phenotype_GeneLocAnno.Total.5perc.fc.gz.qqnorm_AllChrom.txt ../data/Li_eQTLs/unexplained_FDR10.sort_FIXED.txt  ../data/overlapeQTL_try2/apaTotal_unexplainedQTLs.txt

python getAPAfromanyeQTL.py ../data/apaQTLNominal_4pc/APApeak_Phenotype_GeneLocAnno.Nuclear.5perc.fc.gz.qqnorm_AllChrom.txt ../data/Li_eQTLs/explained_FDR10.sort_FIXED.txt  ../data/overlapeQTL_try2/apaNuclear_explainedQTLs.txt

python getAPAfromanyeQTL.py ../data/apaQTLNominal_4pc/APApeak_Phenotype_GeneLocAnno.Nuclear.5perc.fc.gz.qqnorm_AllChrom.txt ../data/Li_eQTLs/unexplained_FDR10.sort_FIXED.txt  ../data/overlapeQTL_try2/apaNuclear_unexplainedQTLs.txt

total

I can group the unexplained by gene and snp then I can ask if there is at least 1 significat peak for each of these.

nomnames=c("peakID", 'snp','dist', 'pval', 'slope')
totalapaUnexplained=read.table("../data/overlapeQTL_try2/apaTotal_unexplainedQTLs.txt", stringsAsFactors = F, col.names = nomnames) %>% separate(peakID, into=c("chr","start","end","geneID"), sep=":") %>% separate(geneID, into=c("gene", "loc", "strand", "PASnum"), sep="_") %>% group_by(gene, snp) %>% slice(which.min(pval))

totalapaUnexplained_sig= totalapaUnexplained %>% filter(pval<.05)

Proportion explained:

nrow(totalapaUnexplained_sig)/nrow(totalapaUnexplained)
[1] 0.3532819

I tested 518 unexplained eQTLs in the total fraction and 183 have a nominally significant peak.

Compare to explained eQTLS:

totalapaexplained=read.table("../data/overlapeQTL_try2/apaTotal_explainedQTLs.txt", stringsAsFactors = F, col.names = nomnames) %>% separate(peakID, into=c("chr","start","end","geneID"), sep=":") %>% separate(geneID, into=c("gene", "loc", "strand", "PASnum"), sep="_") %>% group_by(gene, snp) %>% slice(which.min(pval))

totalapaexplained_sig= totalapaexplained %>% filter(pval<.05)

nrow(totalapaexplained_sig)/nrow(totalapaexplained)
[1] 0.3045326

I am testing 706 explained eQTLs and of those 215 have a nominally significant apaQTL.

difference of proportions:

prop.test(x=c(nrow(totalapaUnexplained_sig),nrow(totalapaexplained_sig)), n=c(nrow(totalapaUnexplained),nrow(totalapaexplained)))

    2-sample test for equality of proportions with continuity
    correction

data:  c(nrow(totalapaUnexplained_sig), nrow(totalapaexplained_sig)) out of c(nrow(totalapaUnexplained), nrow(totalapaexplained))
X-squared = 3.0175, df = 1, p-value = 0.08237
alternative hypothesis: two.sided
95 percent confidence interval:
 -0.006279092  0.103777643
sample estimates:
   prop 1    prop 2 
0.3532819 0.3045326 

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 forcats_0.3.0   stringr_1.3.1   dplyr_0.8.0.1  
 [5] purrr_0.3.2     readr_1.3.1     tidyr_0.8.3     tibble_2.1.1   
 [9] 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   modelr_0.1.2     magrittr_1.5    
[37] whisker_0.3-2    backports_1.1.2  scales_1.0.0     htmltools_0.3.6 
[41] rvest_0.3.2      assertthat_0.2.0 colorspace_1.3-2 stringi_1.2.4   
[45] lazyeval_0.2.1   munsell_0.5.0    broom_0.5.1      crayon_1.3.4