Last updated: 2020-02-28

Checks: 7 0

Knit directory: apaQTL/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.


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

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:    data/ProSeq/
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  .Rprofile
    Untracked:  ._.DS_Store
    Untracked:  .gitignore
    Untracked:  @
    Untracked:  GEO_brimittleman/
    Untracked:  _workflowr.yml
    Untracked:  analysis/._PASdescriptiveplots.Rmd
    Untracked:  analysis/._cuttoffPercUsage.Rmd
    Untracked:  analysis/APApeak_Phenotype_GeneLocAnno.Nuclear.5perc.fc.gz.qqnorm.allChrom
    Untracked:  analysis/APApeak_Phenotype_GeneLocAnno.Total.5perc.fc.gz.qqnorm.allChrom
    Untracked:  analysis/QTLexampleplots.Rmd
    Untracked:  analysis/cuttoffPercUsage.Rmd
    Untracked:  analysis/eQTLoverlap.Rmd
    Untracked:  analysis/interpret verify bam.Rmd
    Untracked:  analysis/interpret_verifybam.Rmd
    Untracked:  analysis/mergeRNA.Rmd
    Untracked:  analysis/oldstuffNotNeeded.Rmd
    Untracked:  analysis/remove_badlines.Rmd
    Untracked:  analysis/totSpecInNuclear.Rmd
    Untracked:  analysis/totSpecIncludenotTested.Rmd
    Untracked:  analysis/totalspec.Rmd
    Untracked:  apaQTL.Rproj
    Untracked:  checksumsfastq.txt.gz
    Untracked:  code/.NascentRNAdtPlotFirstintronicPAS.sh.swp
    Untracked:  code/._Allsplicesite2fasta.py
    Untracked:  code/._ApaQTL_nominalNonnorm.sh
    Untracked:  code/._BothFracDTPlotGeneRegions.sh
    Untracked:  code/._BothFracDTPlotGeneRegions_normalized.sh
    Untracked:  code/._ClosestTissuePAS.sh
    Untracked:  code/._ColocApAeQTL.sh
    Untracked:  code/._ColocApAeQTL_PM.sh
    Untracked:  code/._Coloc_generalAPAeQTL.R
    Untracked:  code/._Coloc_generalAPAeQTL_PM.R
    Untracked:  code/._CreateRNALZforeQTLs.sh
    Untracked:  code/._CreateRNALZnucAPAqtls.sh
    Untracked:  code/._DistPAS2Sig_RandomIntron.py
    Untracked:  code/._EandPqtl_perm.sh
    Untracked:  code/._EandPqtls.sh
    Untracked:  code/._ExtractGene4eQTLLZ.py
    Untracked:  code/._ExtractGene4eQTLLZpy
    Untracked:  code/._ExtractGeneRNAAssoc.py
    Untracked:  code/._ExtractPAS4LZeQTLs.py
    Untracked:  code/._ExtractPAS4eQTLsLZ.sh
    Untracked:  code/._ExtractPASforLZ.py
    Untracked:  code/._ExtractPASforLZ_run.sh
    Untracked:  code/._FC_NucintornUpandDown.sh
    Untracked:  code/._FC_UTR.sh
    Untracked:  code/._FC_intornUpandDownsteamPAS.sh
    Untracked:  code/._FC_nascentseq.sh
    Untracked:  code/._FC_newPeaks_olddata.sh
    Untracked:  code/._HMMpermuteTotal.py
    Untracked:  code/._HmmPermute.py
    Untracked:  code/._IntronicPASDT.sh
    Untracked:  code/._LC_samplegroups.py
    Untracked:  code/._LD_qtl.sh
    Untracked:  code/._LD_snpsproxy.sh
    Untracked:  code/._MapAllRBP.sh
    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/._NomResfromPASSNP.py
    Untracked:  code/._NuclearPAS_5per.bed.py
    Untracked:  code/._NuclearandRNA5samp_dtplots.sh
    Untracked:  code/._PTTfacetboxplots.R
    Untracked:  code/._PrematureQTLNominal.sh
    Untracked:  code/._PrematureQTLPermuted.sh
    Untracked:  code/._QTL2bed.py
    Untracked:  code/._QTL2bed_withstrand.py
    Untracked:  code/._RBPdisrupt.sh
    Untracked:  code/._RNAbam2bw.sh
    Untracked:  code/._RNAseqDTplot.sh
    Untracked:  code/._Randomsplicesite2fasta.py
    Untracked:  code/._Rplots.pdf
    Untracked:  code/._RunRes2PAS.sh
    Untracked:  code/._SAF215upbed.py
    Untracked:  code/._SnakefilePAS
    Untracked:  code/._SnakefilefiltPAS
    Untracked:  code/._TESplots100bp.sh
    Untracked:  code/._TESplots150bp.sh
    Untracked:  code/._TESplots200bp.sh
    Untracked:  code/._TotalPAS_5perc.bed.py
    Untracked:  code/._Untitled
    Untracked:  code/._ZipandTabPheno.sh
    Untracked:  code/._aAPAqtl_nominal39ind.sh
    Untracked:  code/._allNucSpecQTLine.py
    Untracked:  code/._allNucSpecfromNonNorm.py
    Untracked:  code/._annotatePacBioPASregion.sh
    Untracked:  code/._annotatedPAS2bed.py
    Untracked:  code/._apaInPandE.py
    Untracked:  code/._apaQTLCorrectPvalMakeQQ.R
    Untracked:  code/._apaQTLCorrectpval_6or7a.R
    Untracked:  code/._apaQTL_Nominal.sh
    Untracked:  code/._apaQTL_nominalInclusive.sh
    Untracked:  code/._apaQTL_nominalv67.sh
    Untracked:  code/._apaQTL_permuted.sh
    Untracked:  code/._apaQTL_permuted_test6A7A.sh
    Untracked:  code/._apainRibo.py
    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/._changeRibonomQTLres2genename.py
    Untracked:  code/._changenomQTLres2geneName.py
    Untracked:  code/._chooseAnno2PAS_pacbio.py
    Untracked:  code/._chooseAnno2SAF.py
    Untracked:  code/._chooseSignalSite
    Untracked:  code/._chooseSignalSite.py
    Untracked:  code/._closestannotated.sh
    Untracked:  code/._closestannotated_byfrac.sh
    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/._convertNominal2SNPloc2Versions.py
    Untracked:  code/._convertNumeric.py
    Untracked:  code/._correctNomeqtl.R
    Untracked:  code/._createPlinkSampfile.py
    Untracked:  code/._dag.pdf
    Untracked:  code/._eQTL_switch2snploc.py
    Untracked:  code/._eQTLgenestestedapa.py
    Untracked:  code/._encodeRNADTplots.sh
    Untracked:  code/._extactPAS100meanphyloP.py
    Untracked:  code/._extractGeneLZfiles.sh
    Untracked:  code/._extractGeneLZfileseQTLs.sh
    Untracked:  code/._extractGenotypes.py
    Untracked:  code/._extractPACmeanPhyloP.py
    Untracked:  code/._extractPhylop50up.py
    Untracked:  code/._extractPhylopextra50.py
    Untracked:  code/._extractRNApval4lz.py
    Untracked:  code/._extractseqfromqtlfastq.py
    Untracked:  code/._fc2leafphen.py
    Untracked:  code/._fc_filteredPAS6and7As.sh
    Untracked:  code/._fifteenBPupstreamPAS.py
    Untracked:  code/._fiftyBPupstreamPAS.py
    Untracked:  code/._filter5perc.R
    Untracked:  code/._filter5percPheno.py
    Untracked:  code/._filterLDsnps.py
    Untracked:  code/._filterMPPAS.py
    Untracked:  code/._filterMPPAS_15.py
    Untracked:  code/._filterMPPAS_15_7As.py
    Untracked:  code/._filterMPPAS_50.py
    Untracked:  code/._filterSAFforMP.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/._fixFChead_short.py
    Untracked:  code/._fixGWAS4Munge.py
    Untracked:  code/._fixH3k12ac.py
    Untracked:  code/._fixPASregionSNPs.py
    Untracked:  code/._fixRNAhead4corr.py
    Untracked:  code/._fixRNAkalisto.py
    Untracked:  code/._fix_randomIntron.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/._getApapval4eqtl_version67.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/._intersectVCFandupPAS.sh
    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/._mapSSsnps2PAS.sh
    Untracked:  code/._mergRNABam.sh
    Untracked:  code/._mergeAllBam.sh
    Untracked:  code/._mergeAnnotations.sh
    Untracked:  code/._mergeBW_norm.sh
    Untracked:  code/._mergeBamNascent.sh
    Untracked:  code/._mergeByFracBam.sh
    Untracked:  code/._mergePeaks.sh
    Untracked:  code/._miRNAdisrupt.sh
    Untracked:  code/._mnase1stintron.sh
    Untracked:  code/._mnaseDT_fourthintron.sh
    Untracked:  code/._namePeaks.py
    Untracked:  code/._netseqDTplot1stIntron.sh
    Untracked:  code/._netseqFC.sh
    Untracked:  code/._nucQTLGWAS.py
    Untracked:  code/._nucSpecQTLineData.py
    Untracked:  code/._nucSpeceffectsize.py
    Untracked:  code/._nucspecnucPASine.py
    Untracked:  code/._pQTLsotherdata.py
    Untracked:  code/._pacbioDT.sh
    Untracked:  code/._pacbioIntronicDT.sh
    Untracked:  code/._parseALLSSres.py
    Untracked:  code/._parseBestbamid.py
    Untracked:  code/._parseLDRes.py
    Untracked:  code/._parseLDresBothPAS.sh
    Untracked:  code/._parseRanodmSSres.py
    Untracked:  code/._parseSSres.py
    Untracked:  code/._peak2PAS.py
    Untracked:  code/._peakFC.sh
    Untracked:  code/._pheno2countonly.R
    Untracked:  code/._phenoQTLfromlist.py
    Untracked:  code/._processYRIgen.py
    Untracked:  code/._pttQTLsinapaQTL.py
    Untracked:  code/._qtlRegionseq.sh
    Untracked:  code/._qtlsPvalOppFrac.py
    Untracked:  code/._quantassign2parsedpeak.py
    Untracked:  code/._removeXfromHmm.py
    Untracked:  code/._removeloc_pheno.py
    Untracked:  code/._riboQTL.sh
    Untracked:  code/._runCorrectNomEqtl.sh
    Untracked:  code/._runFixGWAS4Munge.sh
    Untracked:  code/._runHMMpermuteAPAqtls.sh
    Untracked:  code/._runHMMpermuteeQTLS.sh
    Untracked:  code/._runMakeEmpiricaleQTL_unexp.sh
    Untracked:  code/._runMakeeQTLempirical.sh
    Untracked:  code/._run_bam2bw_all3prime.sh
    Untracked:  code/._run_bam2bw_extra3.sh
    Untracked:  code/._run_bestbamid.sj
    Untracked:  code/._run_dist2sig_randomintron.sh
    Untracked:  code/._run_filtersnpLD.sh
    Untracked:  code/._run_getAPAfromeQTL_version6.7.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_prxySNP.sh
    Untracked:  code/._run_pttfacetboxplot.sh
    Untracked:  code/._run_sepUsagephen.sh
    Untracked:  code/._run_sepgenobychrom.sh
    Untracked:  code/._run_verifybam.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/._specAPAinE.py
    Untracked:  code/._splicesite2fasta.py
    Untracked:  code/._submit-snakemakePAS.sh
    Untracked:  code/._submit-snakemakefiltPAS.sh
    Untracked:  code/._subsetAPAnotEorPgene.py
    Untracked:  code/._subsetAPAnotEorPgene_2versions.py
    Untracked:  code/._subsetAPAnotEorR.py
    Untracked:  code/._subsetApanoteGene.py
    Untracked:  code/._subsetApanoteGene_2versions.py
    Untracked:  code/._subsetNootherQTL.py
    Untracked:  code/._subsetUnexplainedeQTLs.py
    Untracked:  code/._subsetVCF_SS.sh
    Untracked:  code/._subsetVCF_noSSregions.sh
    Untracked:  code/._subsetVCF_upstreamPAS.sh
    Untracked:  code/._subset_diffisopheno.py
    Untracked:  code/._subsetpermAPAwithGenelist.py
    Untracked:  code/._subsetpermAPAwithGenelist_2versions.py
    Untracked:  code/._subsetvcf_otherreg.sh
    Untracked:  code/._subsetvcf_permSS.sh
    Untracked:  code/._subtrachfiveprimeUTR.sh
    Untracked:  code/._subtractExons.sh
    Untracked:  code/._subtractfiveprimeUTR.sh
    Untracked:  code/._tabixSNPS.sh
    Untracked:  code/._tenBPupstreamPAS.py
    Untracked:  code/._test.pdf
    Untracked:  code/._testVerifyBam.sh
    Untracked:  code/._tissuePAS2hg19.sh
    Untracked:  code/._totSeceffectsize.py
    Untracked:  code/._twentyBPupstreamPAS.py
    Untracked:  code/._utrdms2saf.py
    Untracked:  code/._vcf2bed.py
    Untracked:  code/._verifyBam18517N.sh
    Untracked:  code/._verifyBam18517T.sh
    Untracked:  code/._verifyBam19128N.sh
    Untracked:  code/._verifyBam19128T.sh
    Untracked:  code/._wrap_verifybam.sh
    Untracked:  code/._writePTTexamplecode.py
    Untracked:  code/._writePTTexamplecode.sh
    Untracked:  code/.pversion
    Untracked:  code/.snakemake/
    Untracked:  code/1
    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_inclusive.err
    Untracked:  code/APAqtl_nominal_inclusive.out
    Untracked:  code/APAqtl_nominal_nonNorm.err
    Untracked:  code/APAqtl_nominal_nonNorm.out
    Untracked:  code/APAqtl_nominal_versions67.err
    Untracked:  code/APAqtl_nominal_versions67.out
    Untracked:  code/APAqtl_permuted.err
    Untracked:  code/APAqtl_permuted.out
    Untracked:  code/APAqtl_permuted_versions67.err
    Untracked:  code/APAqtl_permuted_versions67.out
    Untracked:  code/Allsplicesite2fasta.py
    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/ClosestTissuePAS.sh
    Untracked:  code/ColocApAeQTL.err
    Untracked:  code/ColocApAeQTL.out
    Untracked:  code/ColocApAeQTL.sh
    Untracked:  code/ColocApAeQTLPM.err
    Untracked:  code/ColocApAeQTLPM.out
    Untracked:  code/ColocApAeQTL_PM.sh
    Untracked:  code/Coloc_generalAPAeQTL.R
    Untracked:  code/Coloc_generalAPAeQTL_PM.R
    Untracked:  code/CreateRNALZforeQTLs.sh
    Untracked:  code/CreateRNALZnucAPAqtls.sh
    Untracked:  code/DistPAS2Sig_RandomIntron.py
    Untracked:  code/EandPqtl.err
    Untracked:  code/EandPqtl.out
    Untracked:  code/EncodeRNADTPlotGeneRegions.err
    Untracked:  code/EncodeRNADTPlotGeneRegions.out
    Untracked:  code/ExtractGene4eQTLLZ.py
    Untracked:  code/ExtractGene4eQTLLZpy
    Untracked:  code/ExtractGeneRNAAssoc.py
    Untracked:  code/ExtractPAS4LZeQTLs.py
    Untracked:  code/ExtractPAS4eQTLsLZ.sh
    Untracked:  code/ExtractPASforLZ.py
    Untracked:  code/ExtractPASforLZ_run.sh
    Untracked:  code/FC_NucintronPASupandDown.err
    Untracked:  code/FC_NucintronPASupandDown.out
    Untracked:  code/FC_UTR.err
    Untracked:  code/FC_UTR.out
    Untracked:  code/FC_intronPASupandDown.err
    Untracked:  code/FC_intronPASupandDown.out
    Untracked:  code/FC_nascent.err
    Untracked:  code/FC_nascentout
    Untracked:  code/FC_newPAS_olddata.err
    Untracked:  code/FC_newPAS_olddata.out
    Untracked:  code/HmmPermute.p
    Untracked:  code/IntronicPASDT.err
    Untracked:  code/IntronicPASDT.out
    Untracked:  code/LD_vcftools.hap.out
    Untracked:  code/MapAllRBP.sh
    Untracked:  code/MapRBP.err
    Untracked:  code/MapRBP.out
    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/Nuclear_example.err
    Untracked:  code/Nuclear_example.out
    Untracked:  code/NuclearandRNA5samp_dtplots.sh
    Untracked:  code/NuclearandRNAFracDTPlotGeneRegions.err
    Untracked:  code/NuclearandRNAFracDTPlotGeneRegions.out
    Untracked:  code/PACbioDT.err
    Untracked:  code/PACbioDT.out
    Untracked:  code/PACbioDTitronic.err
    Untracked:  code/PACbioDTitronic.out
    Untracked:  code/Prematureqtl_nominal.err
    Untracked:  code/Prematureqtl_nominal.out
    Untracked:  code/Prematureqtl_permuted.err
    Untracked:  code/Prematureqtl_permuted.out
    Untracked:  code/RBPdisrupt.err
    Untracked:  code/RBPdisrupt.out
    Untracked:  code/RBPdisrupt.sh
    Untracked:  code/README.md
    Untracked:  code/RNABam2BW.err
    Untracked:  code/RNABam2BW.out
    Untracked:  code/RNAseqDTPlotGeneRegions.err
    Untracked:  code/RNAseqDTPlotGeneRegions.out
    Untracked:  code/Randomsplicesite2fasta.py
    Untracked:  code/Rplots.pdf
    Untracked:  code/TESplots100bp.err
    Untracked:  code/TESplots100bp.out
    Untracked:  code/TESplots150bp.err
    Untracked:  code/TESplots150bp.out
    Untracked:  code/TESplots200bp.err
    Untracked:  code/TESplots200bp.out
    Untracked:  code/Tissueclosestannotated.err
    Untracked:  code/Tissueclosestannotated.out
    Untracked:  code/Total_example.err
    Untracked:  code/Total_example.out
    Untracked:  code/Untitled
    Untracked:  code/YRI_LCL.vcf.gz
    Untracked:  code/YRI_LCL_chr1.vcf.gz.log
    Untracked:  code/YRI_LCL_chr1.vcf.gz.recode.vcf
    Untracked:  code/annotatedPASregion.err
    Untracked:  code/annotatedPASregion.out
    Untracked:  code/apaQTL_nominalInclusive.sh
    Untracked:  code/assignPeak2Intronicregion.err
    Untracked:  code/assignPeak2Intronicregion.out
    Untracked:  code/assigntotPeak2Intronicregion.err
    Untracked:  code/assigntotPeak2Intronicregion.out
    Untracked:  code/bam2bw.err
    Untracked:  code/bam2bw.out
    Untracked:  code/bam2bw_5primemost.err
    Untracked:  code/bam2bw_5primemost.out
    Untracked:  code/binary_fileset.log
    Untracked:  code/bothFrac_FC.err
    Untracked:  code/bothFrac_FC.out
    Untracked:  code/callSHscripts.txt
    Untracked:  code/closestannotated.err
    Untracked:  code/closestannotated.out
    Untracked:  code/closestannotatedbyfrac.err
    Untracked:  code/closestannotatedbyfrac.out
    Untracked:  code/dag.pdf
    Untracked:  code/dagPAS.pdf
    Untracked:  code/dagfiltPAS.pdf
    Untracked:  code/extactPAS100meanphyloP.py
    Untracked:  code/extractGeneLZfiles.err
    Untracked:  code/extractGeneLZfiles.out
    Untracked:  code/extractGeneLZfiles.sh
    Untracked:  code/extractGeneLZfileseQTLs.err
    Untracked:  code/extractGeneLZfileseQTLs.out
    Untracked:  code/extractGeneLZfileseQTLs.sh
    Untracked:  code/extractPACmeanPhyloP.py
    Untracked:  code/extractPASLZfiles.err
    Untracked:  code/extractPASLZfiles.out
    Untracked:  code/extractPASLZfileseQTLs.err
    Untracked:  code/extractPASLZfileseQTLs.out
    Untracked:  code/extractPhylop50up.py
    Untracked:  code/extractPhylopextra50.py
    Untracked:  code/extractRNApval4lz.py
    Untracked:  code/fixExandUnexeQTL
    Untracked:  code/fixGWAS4Munge.py
    Untracked:  code/fix_randomIntron.py
    Untracked:  code/fixmunge
    Untracked:  code/genotypesYRI.gen.proc.keep.vcf.log
    Untracked:  code/genotypesYRI.gen.proc.keep.vcf.recode.vcf
    Untracked:  code/getseq100up.err
    Untracked:  code/getseq100up.out
    Untracked:  code/grouptranscripts.err
    Untracked:  code/grouptranscripts.out
    Untracked:  code/intersectPAS_ssSNPS.err
    Untracked:  code/intersectPAS_ssSNPS.out
    Untracked:  code/intersectVCFPAS.err
    Untracked:  code/intersectVCFPAS.out
    Untracked:  code/liftoverPAShg38to19.err
    Untracked:  code/liftoverPAShg38to19.out
    Untracked:  code/log/
    Untracked:  code/logs/
    Untracked:  code/merge53PRIMEbam.err
    Untracked:  code/merge53PRIMEbam.out
    Untracked:  code/merge53RNAbam.err
    Untracked:  code/merge53prime.sh
    Untracked:  code/merge5RNABam.err
    Untracked:  code/merge5RNABam.out
    Untracked:  code/merge5RNAbam.out
    Untracked:  code/merge5RNAbam.sh
    Untracked:  code/mergeAnno.err
    Untracked:  code/mergeAnno.out
    Untracked:  code/mergeBWnorm.err
    Untracked:  code/mergeBWnorm.out
    Untracked:  code/mergeBamNacent.err
    Untracked:  code/mergeBamNacent.out
    Untracked:  code/mergeRNAbam.err
    Untracked:  code/mergeRNAbam.out
    Untracked:  code/miRNAdisrupt.err
    Untracked:  code/miRNAdisrupt.out
    Untracked:  code/miRNAdisrupt.sh
    Untracked:  code/mnaseDTPlot1stintron.err
    Untracked:  code/mnaseDTPlot1stintron.out
    Untracked:  code/mnaseDTPlot4thintron.err
    Untracked:  code/mnaseDTPlot4thintron.out
    Untracked:  code/netDTPlot4thintron.out
    Untracked:  code/netseqFC.err
    Untracked:  code/netseqFC.out
    Untracked:  code/neyDTPlot4thintron.err
    Untracked:  code/nucspecinE.py
    Untracked:  code/parseALLSSres.py
    Untracked:  code/parseLDRes.py
    Untracked:  code/parseLDres.err
    Untracked:  code/parseLDres.out
    Untracked:  code/parseLDresBothPAS.sh
    Untracked:  code/parseRanodmSSres.py
    Untracked:  code/parseSSres.py
    Untracked:  code/plink.log
    Untracked:  code/prxySNP.err
    Untracked:  code/prxySNP.out
    Untracked:  code/pttFacetBoxplots.err
    Untracked:  code/pttFacetBoxplots.out
    Untracked:  code/qtlFacetBoxplots.err
    Untracked:  code/qtlFacetBoxplots.out
    Untracked:  code/rLD_vcftools.hap.err
    Untracked:  code/riboqtl.err
    Untracked:  code/riboqtl.out
    Untracked:  code/runBestBamID.err
    Untracked:  code/runCorrectNomeqtl.err
    Untracked:  code/runCorrectNomeqtl.out
    Untracked:  code/runFilterLD.err
    Untracked:  code/runFilterLD.out
    Untracked:  code/runFixGWAS4Munge.sh
    Untracked:  code/runHMMpermute.err
    Untracked:  code/runHMMpermute.out
    Untracked:  code/runHMMpermuteeQTLs.err
    Untracked:  code/runHMMpermuteeQTLs.out
    Untracked:  code/runMakeEmpiricaleQTLs.err
    Untracked:  code/runMakeEmpiricaleQTLs.out
    Untracked:  code/runMakeEmpiricaleQTLsunex.err
    Untracked:  code/runMakeEmpiricaleQTLsunex.out
    Untracked:  code/run_DistPAS2Sig.err
    Untracked:  code/run_DistPAS2Sig.out
    Untracked:  code/run_DistPAS2Sig_intron.err
    Untracked:  code/run_DistPAS2Sig_intron.out
    Untracked:  code/run_bam2bw.err
    Untracked:  code/run_bam2bw.out
    Untracked:  code/run_bam2bwexta.err
    Untracked:  code/run_bam2bwexta.out
    Untracked:  code/run_dist2sig_randomintron.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_leafcutter_ds.err
    Untracked:  code/run_leafcutter_ds.out
    Untracked:  code/run_sepgenobychrom.err
    Untracked:  code/run_sepgenobychrom.out
    Untracked:  code/run_sepusage.err
    Untracked:  code/run_sepusage.out
    Untracked:  code/run_verifybam.err
    Untracked:  code/run_verifybam.out
    Untracked:  code/run_verifybam128N.err
    Untracked:  code/run_verifybam128N.out
    Untracked:  code/run_verifybam128T.err
    Untracked:  code/run_verifybam128T.out
    Untracked:  code/run_verifybam517N.err
    Untracked:  code/run_verifybam517N.out
    Untracked:  code/run_verifybam517T.err
    Untracked:  code/run_verifybam517T.out
    Untracked:  code/runprxySNP.err
    Untracked:  code/runprxySNP.out
    Untracked:  code/runres2pas.err
    Untracked:  code/runres2pas.out
    Untracked:  code/scripts/
    Untracked:  code/scripts_PAS_500_Lymph/
    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/specAPAinE.py
    Untracked:  code/splicesite2fasta.py
    Untracked:  code/subsetAPAnotEorR.py
    Untracked:  code/subsetNootherQTL.py
    Untracked:  code/subsetvcf_SS.err
    Untracked:  code/subsetvcf_SS.out
    Untracked:  code/subsetvcf_noSS.err
    Untracked:  code/subsetvcf_noSS.out
    Untracked:  code/subsetvcf_pas.err
    Untracked:  code/subsetvcf_pas.out
    Untracked:  code/subsetvcf_perm.err
    Untracked:  code/subsetvcf_perm.out
    Untracked:  code/subsetvcf_rand.err
    Untracked:  code/subsetvcf_rand.out
    Untracked:  code/subtract5UTR.err
    Untracked:  code/subtract5UTR.out
    Untracked:  code/subtractExons.err
    Untracked:  code/subtractExons.out
    Untracked:  code/tabixSNPs.err
    Untracked:  code/tabixSNPs.out
    Untracked:  code/test.pdf
    Untracked:  code/testFix.txt
    Untracked:  code/test_verifybam.err
    Untracked:  code/test_verifybam.out
    Untracked:  code/tissuePAS2hg19.sh
    Untracked:  code/vcf_keepsnps.err
    Untracked:  code/vcf_keepsnps.out
    Untracked:  code/wrap_verifybam.err
    Untracked:  code/wrap_verifybam.out
    Untracked:  code/zipandtabPhen.err
    Untracked:  code/zipandtabPhen.out
    Untracked:  data/._.DS_Store
    Untracked:  data/._MetaDataSequencing.txt
    Untracked:  data/AnnotatedPAS/
    Untracked:  data/ApaByEgene/
    Untracked:  data/ApaByPgene/
    Untracked:  data/ApaByRgene/
    Untracked:  data/BadLines/
    Untracked:  data/BaseComp/
    Untracked:  data/Battle_pQTL/
    Untracked:  data/CheckSums/
    Untracked:  data/CompareOldandNew/
    Untracked:  data/DTmatrix/
    Untracked:  data/DiffIso/
    Untracked:  data/EncodeRNA/
    Untracked:  data/ExampleQTLPlots/
    Untracked:  data/ExampleQTLPlots_update/
    Untracked:  data/ExpressionIndependentapaQTLs.txt
    Untracked:  data/FiveMergedBW/
    Untracked:  data/FiveMergedBam/
    Untracked:  data/FlaggedPAS/
    Untracked:  data/GWAS_overlap/
    Untracked:  data/Geuvadis/
    Untracked:  data/GeuvadisRNA/
    Untracked:  data/GeuvadiseQTL/
    Untracked:  data/HMMqtls/
    Untracked:  data/LDSR_annotations/
    Untracked:  data/LZ_both/
    Untracked:  data/Li_eQTLs/
    Untracked:  data/NMD/
    Untracked:  data/NascentRNA/
    Untracked:  data/NucSpeceQTLeffect/
    Untracked:  data/PAS/
    Untracked:  data/PAS_postFlag/
    Untracked:  data/PolyA_DB/
    Untracked:  data/PreTerm_pheno/
    Untracked:  data/PrematureQTLNominal/
    Untracked:  data/PrematureQTLPermuted/
    Untracked:  data/QTLGenotypes/
    Untracked:  data/QTLoverlap/
    Untracked:  data/QTLoverlap_inclusive/
    Untracked:  data/QTLoverlap_nonNorm/
    Untracked:  data/README.md
    Untracked:  data/RNAseq/
    Untracked:  data/Reads2UTR/
    Untracked:  data/SNPinSS/
    Untracked:  data/SignalSiteFiles/
    Untracked:  data/TF_motifdisruption/
    Untracked:  data/TSS/
    Untracked:  data/ThirtyNineIndQtl_nominal/
    Untracked:  data/TissueData/
    Untracked:  data/Version15bp6As/
    Untracked:  data/Version15bp7As/
    Untracked:  data/apaQTLNominal/
    Untracked:  data/apaQTLNominal_4pc/
    Untracked:  data/apaQTLNominal_inclusive/
    Untracked:  data/apaQTLPermuted/
    Untracked:  data/apaQTLPermuted_4pc/
    Untracked:  data/apaQTLs/
    Untracked:  data/assignedPeaks/
    Untracked:  data/assignedPeaks_15Up/
    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/
    Untracked:  data/bw_norm/
    Untracked:  data/coloc/
    Untracked:  data/coloc_PM/
    Untracked:  data/eCLip/
    Untracked:  data/eQTL_LZ/
    Untracked:  data/eQTLs/
    Untracked:  data/exampleQTLs/
    Untracked:  data/exosome/
    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/locusZoom/
    Untracked:  data/mergedBG/
    Untracked:  data/mergedBW_byfrac/
    Untracked:  data/mergedBW_norm/
    Untracked:  data/mergedBam/
    Untracked:  data/mergedbyFracBam/
    Untracked:  data/miRNAbinding/
    Untracked:  data/molPhenos/
    Untracked:  data/molQTLs/
    Untracked:  data/motifdistrupt/
    Untracked:  data/nPAS/
    Untracked:  data/netseq/
    Untracked:  data/nonNorm_pheno/
    Untracked:  data/nuc_10up/
    Untracked:  data/nuc_10upclean/
    Untracked:  data/oldPASfiles/
    Untracked:  data/overlapeQTL_try2/
    Untracked:  data/overlapeQTLs/
    Untracked:  data/pQTLoverlap/
    Untracked:  data/pacbio/
    Untracked:  data/peakCoverage/
    Untracked:  data/peaks_5perc/
    Untracked:  data/phenotype/
    Untracked:  data/phenotype_5perc/
    Untracked:  data/phenotype_inclusivePAS/
    Untracked:  data/phylop/
    Untracked:  data/pttQTL/
    Untracked:  data/pttQTLplots/
    Untracked:  data/sigDiffGenes.txt
    Untracked:  data/sort/
    Untracked:  data/sort_clean/
    Untracked:  data/sort_waspfilter/
    Untracked:  data/splicesite/
    Untracked:  data/twoMech/
    Untracked:  data/vareQTLvarAPAqtl/
    Untracked:  data/verifyBAM/
    Untracked:  data/verifyBAM_full/
    Untracked:  nohup.out
    Untracked:  output/._.DS_Store
    Untracked:  output/._AverageDiffHeatmap.Nuclear.png
    Untracked:  output/._AverageDiffHeatmap.Total.png
    Untracked:  output/._GeneswithAPApotential.png
    Untracked:  output/._GeneswithAPApotentialAllPAS.png
    Untracked:  output/._PASlocation.png
    Untracked:  output/._SignalSitePlot.png
    Untracked:  output/._meanCorrelationPhenotypes.svg
    Untracked:  output/._qqplot_Nuclear_APAperm.png
    Untracked:  output/._qqplot_Nuclear_APAperm_4pc.png
    Untracked:  output/._qqplot_Total_APAperm.png
    Untracked:  output/._qqplot_Total_APAperm_4pc.png
    Untracked:  output/AverageDiffHeatmap.Nuclear.png
    Untracked:  output/AverageDiffHeatmap.Total.png
    Untracked:  output/GeneswithAPApotential.png
    Untracked:  output/GeneswithAPApotentialAllPAS.png
    Untracked:  output/PASlocation.png
    Untracked:  output/SignalSitePlot.png
    Untracked:  output/SignalSitePlotbyLoc.png
    Untracked:  output/dtPlots/
    Untracked:  output/fastqc/
    Untracked:  output/meanCorrelationPhenotypes.svg
    Untracked:  output/newnuc.png
    Untracked:  output/newtot.png
    Untracked:  output/oldnuc.png
    Untracked:  output/oldtot.png
    Untracked:  output/qqplot_Nuclear_APAperm.png
    Untracked:  output/qqplot_Nuclear_APAperm_4pc.png
    Untracked:  output/qqplot_Total_APAperm.png
    Untracked:  output/qqplot_Total_APAperm_4pc.png
    Untracked:  run_verifybam517N.err
    Untracked:  run_verifybam517N.out

Unstaged changes:
    Modified:   analysis/ExploreNpas.Rmd
    Modified:   analysis/NuclearSpecIncludeNotTested.Rmd
    Modified:   analysis/PASdescriptiveplots.Rmd
    Modified:   analysis/Readdistagainstfeatures.Rmd
    Modified:   analysis/TSS.Rmd
    Modified:   analysis/apabyeQTLstatus.Rmd
    Modified:   analysis/decayAndStability.Rmd
    Modified:   analysis/miRNAdisrupt.Rmd
    Modified:   analysis/nascenttranscription.Rmd
    Modified:   analysis/nucSpecinEQTLs.Rmd
    Modified:   analysis/overlapapaqtlsandeqtls.Rmd
    Modified:   analysis/pQTLexampleplot.Rmd
    Modified:   analysis/version15bpfilter.Rmd
    Modified:   code/DistPAS2Sig.py
    Modified:   code/Script4NuclearQTLexamples.sh
    Modified:   code/Script4TotalQTLexamples.sh
    Modified:   code/apaQTLsnake.err
    Modified:   code/environment.yaml
    Modified:   code/run_qtlFacetBoxplots.sh
    Deleted:    code/test.txt
    Deleted:    reads_graphs.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 e5dbb2f brimittleman 2020-02-28 add all lines in 1
html f19db64 brimittleman 2020-02-28 Build site.
Rmd 2969449 brimittleman 2020-02-28 add all lines in 1
html 11ea802 brimittleman 2020-02-27 Build site.
Rmd 7449f09 brimittleman 2020-02-27 add figure spec
html 1ca62a2 brimittleman 2020-02-20 Build site.
Rmd 662a604 brimittleman 2020-02-20 add riboqq and PM coloc

In the paper I have qqPlots where I took the apaQTL data and subset it by QTL sets. I never did this for riboQTLs. I will get the riboQTLs from Battle et al and remake the plot including these.

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()
geneNames=read.table("../../genome_anotation_data/ensemble_to_genename.txt", sep="\t", col.names = c('ENSG', 'GeneName', 'source' ),stringsAsFactors = F, header = T)

riboRes=read.table("../data/Battle_pQTL/riboQTLs_battle.txt", header = T,stringsAsFactors = F) %>% inner_join(geneNames,by="ENSG") 

exPe=read.table("../data/Li_eQTLs/explainedEgenes.txt", col.names = "GeneName")
UexPe=read.table("../data/Li_eQTLs/UnexplainedEgenes.txt",col.names = "GeneName")

allE=exPe %>% full_join(UexPe,by="GeneName")
Warning: Column `GeneName` joining factors with different levels, coercing
to character vector
riboRes$bh=p.adjust(riboRes$perm.p.values, method="fdr")

riboRes_sig= riboRes %>% filter(-log10(bh)>=1)

riboGenes=riboRes_sig %>% select(GeneName) %>% anti_join(allE)
Joining, by = "GeneName"
write.table(riboGenes, file="../data/Battle_pQTL/RiboQTLGeneNames.txt", row.names = F, col.names = F, quote = F, sep="\t")
mkdir ../data/ApaByRgene

python subsetpermAPAwithGenelist.py ../data/Battle_pQTL/RiboQTLGeneNames.txt Nuclear ../data/ApaByRgene/NuclearApaRGenes.txt

python subsetpermAPAwithGenelist.py ../data/Battle_pQTL/RiboQTLGeneNames.txt Total ../data/ApaByRgene/TotalApaRGenes.txt

python subsetAPAnotEorR.py Nuclear ../data/ApaByRgene/NotRorE_nuclear.txt
python subsetAPAnotEorR.py Total ../data/ApaByRgene/NotRorE_total.txt
tot.notEorR=read.table("../data/ApaByRgene/NotRorE_total.txt",stringsAsFactors = F,col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval"))
tot.RS=read.table("../data/ApaByRgene/TotalApaRGenes.txt",stringsAsFactors = F,col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval"))
tot.ES=read.table("../data/ApaByPgene/TotalApaESGenes.txt",stringsAsFactors = F, col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval") )
tot.ex=read.table("../data/ApaByEgene/TotalApaexplainedeGenes.txt",stringsAsFactors = F,col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval"))
tot.un=read.table("../data/ApaByEgene/TotalApaUnexplainedeGenes.txt",stringsAsFactors = F, col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval") )

tot_allE=as.data.frame(rbind(tot.ex,tot.un))
tot.RS=na.omit(tot.RS)
tot.notEorR=na.omit(tot.notEorR)
tot.ES=na.omit(tot.ES)
tot.un=na.omit(tot.un)
qqplot(-log10(runif(nrow(tot.notEorR))), -log10(tot.notEorR$bpval), xlab="-log10(Uniform)", ylab="-log10(beta pval)", main="Total Apa")
points(sort(-log10(runif(nrow(tot.RS)))), sort(-log10(tot.RS$bpval)),col= alpha("Red"))
points(sort(-log10(runif(nrow(tot_allE)))), sort(-log10(tot_allE$bpval)),col= alpha("blue"))
abline(0,1)

legend("topleft", legend=c("Neither eGenes nor rGenes", "rGenes", "eGenes"),col=c("black", "red","blue"), pch=16,bty = 'n')

Version Author Date
1ca62a2 brimittleman 2020-02-20
wilcox.test(tot.RS$bpval,tot.notEorR$bpval,alternative="less")

    Wilcoxon rank sum test with continuity correction

data:  tot.RS$bpval and tot.notEorR$bpval
W = 9336600, p-value = 0.0001811
alternative hypothesis: true location shift is less than 0
wilcox.test(tot_allE$bpval,tot.notEorR$bpval,alternative="less")

    Wilcoxon rank sum test with continuity correction

data:  tot_allE$bpval and tot.notEorR$bpval
W = 43090000, p-value = 1.878e-11
alternative hypothesis: true location shift is less than 0
wilcox.test(tot.RS$bpval,tot_allE$bpval,alternative="less")

    Wilcoxon rank sum test with continuity correction

data:  tot.RS$bpval and tot_allE$bpval
W = 1554300, p-value = 0.3891
alternative hypothesis: true location shift is less than 0
nuc.notEorR=read.table("../data/ApaByRgene/NotRorE_nuclear.txt",stringsAsFactors = F,col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval"))
nuc.RS=read.table("../data/ApaByRgene/NuclearApaRGenes.txt",stringsAsFactors = F,col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval"))
nuc.P=read.table("../data/ApaByPgene/NuclearApaPSGenes.txt",stringsAsFactors = F,col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval"))
nuc.ES=read.table("../data/ApaByPgene/NuclearApaESGenes.txt",stringsAsFactors = F, col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval") )
nuc.ex=read.table("../data/ApaByEgene/NuclearApaexplainedeGenes.txt",stringsAsFactors = F,col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval"))
nuc.un=read.table("../data/ApaByEgene/NuclearApaUnexplainedeGenes.txt",stringsAsFactors = F, col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval") )

nuc.un=na.omit(nuc.un)
nuc.RS=na.omit(nuc.RS)
#nuc.notERorP=na.omit(nuc.notERorP)
nuc.P=na.omit(nuc.P)
nuc.notEorR=na.omit(nuc.notEorR)
nuc.ES=na.omit(nuc.ES)
nuc_allE=as.data.frame(rbind(nuc.ex,nuc.un))
qqplot(-log10(runif(nrow(nuc.notEorR))), -log10(nuc.notEorR$bpval), xlab="-log10(Uniform)", ylab="-log10(beta pval)", main="Nuclear Apa")
points(sort(-log10(runif(nrow(nuc.RS)))), sort(-log10(nuc.RS$bpval)),col= alpha("Red"))
points(sort(-log10(runif(nrow(nuc_allE)))), sort(-log10(nuc_allE$bpval)),col= alpha("blue"))
abline(0,1)

legend("topleft", legend=c("Neither eGenes nor rGenes", "rGenes", "eGenes"),col=c("black", "red","blue","green"), pch=16,bty = 'n')

Version Author Date
1ca62a2 brimittleman 2020-02-20
wilcox.test(nuc.RS$bpval,nuc.notEorR$bpval,alternative="less")

    Wilcoxon rank sum test with continuity correction

data:  nuc.RS$bpval and nuc.notEorR$bpval
W = 13007000, p-value = 0.01029
alternative hypothesis: true location shift is less than 0
wilcox.test(nuc_allE$bpval,nuc.notEorR$bpval,alternative="less")

    Wilcoxon rank sum test with continuity correction

data:  nuc_allE$bpval and nuc.notEorR$bpval
W = 57056000, p-value = 6.194e-13
alternative hypothesis: true location shift is less than 0
wilcox.test(nuc.RS$bpval,nuc_allE$bpval,alternative="less")

    Wilcoxon rank sum test with continuity correction

data:  nuc.RS$bpval and nuc_allE$bpval
W = 2189300, p-value = 0.8658
alternative hypothesis: true location shift is less than 0

No QTL at all.

python subsetNootherQTL.py Nuclear ../data/ApaByRgene/NotANY_nuclear.txt
notany_nuc=read.table("../data/ApaByRgene/NotANY_nuclear.txt",stringsAsFactors = F, col.names = c("pid", "nvar", "shape1", "shape2", "dummy", "sid", "dist", "npval", "slope", "ppval", "bpval") )
notany_nuc=na.omit(notany_nuc)
qqplot(-log10(runif(nrow(notany_nuc))), -log10(notany_nuc$bpval), xlab="-log10(Uniform)", ylab="-log10(beta pval)", main="Nuclear Apa")
points(sort(-log10(runif(nrow(nuc_allE)))), sort(-log10(nuc_allE$bpval)),col= alpha("blue"))
points(sort(-log10(runif(nrow(nuc.RS)))), sort(-log10(nuc.RS$bpval)),col= alpha("Red"))
points(sort(-log10(runif(nrow(nuc.P)))), sort(-log10(nuc.P$bpval)),col= alpha("Green"))
abline(0,1)

legend("topleft", legend=c("No other QTL","rGenes", "pGenes","eGenes"),col=c("black", "red","Green","blue"), pch=16,bty = 'n')

Version Author Date
f19db64 brimittleman 2020-02-28

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2       cellranger_1.1.0 plyr_1.8.4       compiler_3.5.1  
 [5] pillar_1.3.1     later_0.7.5      git2r_0.26.1     workflowr_1.6.0 
 [9] tools_3.5.1      digest_0.6.18    lubridate_1.7.4  jsonlite_1.6    
[13] evaluate_0.12    nlme_3.1-137     gtable_0.2.0     lattice_0.20-38 
[17] pkgconfig_2.0.2  rlang_0.4.0      cli_1.1.0        rstudioapi_0.10 
[21] yaml_2.2.0       haven_1.1.2      withr_2.1.2      xml2_1.2.0      
[25] httr_1.3.1       knitr_1.20       hms_0.4.2        generics_0.0.2  
[29] fs_1.3.1         rprojroot_1.3-2  grid_3.5.1       tidyselect_0.2.5
[33] glue_1.3.0       R6_2.3.0         readxl_1.1.0     rmarkdown_1.10  
[37] modelr_0.1.2     magrittr_1.5     whisker_0.3-2    backports_1.1.2 
[41] scales_1.0.0     promises_1.0.1   htmltools_0.3.6  rvest_0.3.2     
[45] assertthat_0.2.0 colorspace_1.3-2 httpuv_1.4.5     stringi_1.2.4   
[49] lazyeval_0.2.1   munsell_0.5.0    broom_0.5.1      crayon_1.3.4