Call QTLs with more inclusive PAS set

Last updated: 2020-03-10

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.

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.

File paths: relative

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

Repository version: 71f66d2

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/._totspecinE.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/totspecinE.py
    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/splicesitestrength.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
html	3af0253	brimittleman	2019-09-17	Build site.
Rmd	f8cb7b8	brimittleman	2019-09-17	move inclusive, get numbers for paper
html	2bc4187	brimittleman	2019-09-15	Build site.
Rmd	7c4debc	brimittleman	2019-09-15	add inclusive PAS 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(qvalue)

I want to call QTLs with all of the PAS to check for specificity.

I can filter the phenotypes in ../data/phenotype by the PAS in

APApeak_Phenotype_GeneLocAnno.Total.fc

allPAS=read.table("../data/PAS/APAPAS_GeneLocAnno.5perc.sort.bed", header=F,col.names=c("chr","start", "end", "ID", "score","strand"),stringsAsFactors = F) %>% separate(ID, into = c("PASnum", "geneID"),sep=":") %>% mutate(PAS_ID=paste("peak", PASnum, sep=""))

TotalPheno:

totalPheo=read.table("../data/phenotype/APApeak_Phenotype_GeneLocAnno.Total.fc",header = T,stringsAsFactors = F) 

totalPheo_peaknum= totalPheo%>% separate(chrom, into=c("chr","start","end", "ID"),sep=":") %>% separate(ID, into=c("gene", "loc", "strand", "PAS_ID"), sep="_") %>% semi_join(allPAS, by="PAS_ID") %>% mutate(ID=paste(gene,loc,strand,PAS_ID,sep="_"), chrom= paste(chr,start,end,ID,sep=":")) %>% select(chrom)

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [12630,
12631, 12632].

totalPheo_filt=totalPheo %>% semi_join(totalPheo_peaknum,by="chrom")

NuclearPheno:

NuclearPheno=read.table("../data/phenotype/APApeak_Phenotype_GeneLocAnno.Nuclear.fc",header = T,stringsAsFactors = F) 

NuclearPheno_peaknum= NuclearPheno%>% separate(chrom, into=c("chr","start","end", "ID"),sep=":") %>% separate(ID, into=c("gene", "loc", "strand", "PAS_ID"), sep="_") %>% semi_join(allPAS, by="PAS_ID") %>% mutate(ID=paste(gene,loc,strand,PAS_ID,sep="_"), chrom= paste(chr,start,end,ID,sep=":")) %>% select(chrom)

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [12630,
12631, 12632].

NuclearPheno_filt=NuclearPheno %>% semi_join(NuclearPheno,by="chrom")

write out:

mkdir ../data/phenotype_inclusivePAS
mkdir ../data/apaQTLNominal_inclusive

write.table(NuclearPheno_filt, row.names = F, col.names = T, "../data/phenotype_inclusivePAS/APApeak_Phenotype_GeneLocAnno.Nuclear.fc", quote=F)

write.table(totalPheo_filt, row.names = F, col.names = T, "../data/phenotype_inclusivePAS/APApeak_Phenotype_GeneLocAnno.Total.fc", quote=F)

#!/bin/bash
#python2 

gzip APApeak_Phenotype_GeneLocAnno.Total.fc
gzip APApeak_Phenotype_GeneLocAnno.Nuclear.fc

python ../../code/prepare_phenotype_table.py APApeak_Phenotype_GeneLocAnno.Total.fc.gz
python ../../code/prepare_phenotype_table.py APApeak_Phenotype_GeneLocAnno.Nuclear.fc.gz

sh APApeak_Phenotype_GeneLocAnno.Nuclear.fc.gz_prepare.sh
sh APApeak_Phenotype_GeneLocAnno.Total.fc.gz_prepare.sh

head -n5 APApeak_Phenotype_GeneLocAnno.Nuclear.fc.gz.PCs > APApeak_Phenotype_GeneLocAnno.Nuclear.fc.gz.4PCs
head -n5 APApeak_Phenotype_GeneLocAnno.Total.fc.gz.PCs > APApeak_Phenotype_GeneLocAnno.Total.fc.gz.4PCs

#code dir
sbatch apaQTL_nominalInclusive.sh

#concatinate res: 

cat ../data/apaQTLNominal_inclusive/APApeak_Phenotype_GeneLocAnno.Total.fc.gz.qqnorm_chr* > ../data/apaQTLNominal_inclusive/APApeak_Phenotype_GeneLocAnno.Total.fc.gz.qqnorm_allChr.txt
cat ../data/apaQTLNominal_inclusive/APApeak_Phenotype_GeneLocAnno.Nuclear.fc.gz.qqnorm_chr* > ../data/apaQTLNominal_inclusive/APApeak_Phenotype_GeneLocAnno.Nuclear.fc.gz.qqnorm_allChr.txt


mkdir ../data/QTLoverlap_inclusive/

python qtlsPvalOppFrac.py ../data/apaQTLs/Total_apaQTLs4pc_5fdr.txt ../data/apaQTLNominal_inclusive/APApeak_Phenotype_GeneLocAnno.Nuclear.fc.gz.qqnorm_allChr.txt ../data/QTLoverlap_inclusive/TotalQTLinNuclearNominal_inc.txt 


python qtlsPvalOppFrac.py ../data/apaQTLs/Nuclear_apaQTLs4pc_5fdr.txt ../data/apaQTLNominal_inclusive/APApeak_Phenotype_GeneLocAnno.Total.fc.gz.qqnorm_allChr.txt ../data/QTLoverlap_inclusive/NuclearQTLinTotalNominal_inc.txt

totAPAinNuc=read.table("../data/QTLoverlap_inclusive/TotalQTLinNuclearNominal_inc.txt", header = F, stringsAsFactors = F, col.names=c("peakID", "snp", "dist", "pval", "slope"))
qval_tot=pi0est(totAPAinNuc$pval, pi0.method = "bootstrap")

nucAPAinTot=read.table("../data/QTLoverlap_inclusive/NuclearQTLinTotalNominal_inc.txt", header = F, stringsAsFactors = F, col.names=c("peakID", "snp", "dist", "pval", "slope"))
qval_nuc=pi0est(nucAPAinTot$pval, pi0.method = "bootstrap")


par(mfrow=c(1,2))
hist(totAPAinNuc$pval, xlab="Nuclear Pvalue", main="Significant Total APA QTLs \n Nuclear")
text(.8,300, paste("pi_1=", round((1-qval_tot$pi0), digit=3), sep=" "))
hist(nucAPAinTot$pval, xlab="Total Pvalue", main="Significant Nuclear APA QTLs \n Total")
text(.8,350, paste("pi_1=", round((1-qval_nuc$pi0), digit=3), sep=" "))

Version	Author	Date
2bc4187	brimittleman	2019-09-15

totAPAinNuc_notsig=totAPAinNuc %>% filter(pval>.05)
nrow(totAPAinNuc_notsig)

[1] 97

nucAPAinTot_notsig=nucAPAinTot %>% filter(pval>.05)
nrow(nucAPAinTot_notsig)

[1] 151

prop.test(x=c(97,151),n=c(443,603), alternative="less")


    2-sample test for equality of proportions with continuity
    correction

data:  c(97, 151) out of c(443, 603)
X-squared = 1.2283, df = 1, p-value = 0.1339
alternative hypothesis: less
95 percent confidence interval:
 -1.00000000  0.01394063
sample estimates:
   prop 1    prop 2 
0.2189616 0.2504146

location for specific:

totAPAinNuc_notsig_loc=totAPAinNuc_notsig %>% separate(peakID, into=c("chr","start","end", "pasid"), sep=":") %>% separate(pasid, into=c("gene","loc","strand","pas"), sep="_") %>% group_by(loc) %>% summarize(n=n())


totAPAinNuc_notsig_loc

# A tibble: 5 x 2
  loc        n
  <chr>  <int>
1 cds       11
2 end        6
3 intron    25
4 utr3      54
5 utr5       1

25/nrow(totAPAinNuc_notsig)

[1] 0.257732

nucAPAinTot_notsig_loc=nucAPAinTot_notsig %>% separate(peakID, into=c("chr","start","end", "pasid"), sep=":") %>% separate(pasid, into=c("gene","loc","strand","pas"), sep="_") %>% group_by(loc) %>% summarize(n=n())


nucAPAinTot_notsig_loc

# A tibble: 5 x 2
  loc        n
  <chr>  <int>
1 cds        7
2 end       22
3 intron    50
4 utr3      67
5 utr5       5

50/nrow(nucAPAinTot_notsig)

[1] 0.3311258

Look at nuclear specific in eQTL:

nucAPAinTot_notsig_small=nucAPAinTot_notsig %>% separate(peakID, into=c("chr","start","end", "pasid"), sep=":") %>% separate(pasid, into=c("gene","loc","strand","pas"), sep="_") %>% select(gene, pas, snp)

write.table(nucAPAinTot_notsig_small, "../data/QTLoverlap_inclusive/NuclearSpecApaQTLinclusive.txt", col.names=T, row.names=F, quote=F)

Test these is edata:

python nucspecinE.py

nucspecinE=read.table("../data/QTLoverlap_inclusive/NuclearSpecApaQTLinclusive_withE.txt", stringsAsFactors =F, col.names=c("peakID", 'snp','dist', 'pval', 'slope'))

sig=nucspecinE %>% filter(pval<.05)

nrow(sig)

[1] 13

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] qvalue_2.14.0   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] tidyselect_0.2.5 reshape2_1.4.3   splines_3.5.1    haven_1.1.2     
 [5] lattice_0.20-38  colorspace_1.3-2 generics_0.0.2   htmltools_0.3.6 
 [9] yaml_2.2.0       utf8_1.1.4       rlang_0.4.0      later_0.7.5     
[13] pillar_1.3.1     glue_1.3.0       withr_2.1.2      modelr_0.1.2    
[17] readxl_1.1.0     plyr_1.8.4       munsell_0.5.0    gtable_0.2.0    
[21] workflowr_1.6.0  cellranger_1.1.0 rvest_0.3.2      evaluate_0.12   
[25] knitr_1.20       httpuv_1.4.5     fansi_0.4.0      broom_0.5.1     
[29] Rcpp_1.0.2       promises_1.0.1   scales_1.0.0     backports_1.1.2 
[33] jsonlite_1.6     fs_1.3.1         hms_0.4.2        digest_0.6.18   
[37] stringi_1.2.4    grid_3.5.1       rprojroot_1.3-2  cli_1.1.0       
[41] tools_3.5.1      magrittr_1.5     lazyeval_0.2.1   crayon_1.3.4    
[45] whisker_0.3-2    pkgconfig_2.0.2  xml2_1.2.0       lubridate_1.7.4 
[49] assertthat_0.2.0 rmarkdown_1.10   httr_1.3.1       rstudioapi_0.10 
[53] R6_2.3.0         nlme_3.1-137     git2r_0.26.1     compiler_3.5.1

Call QTLs with more inclusive PAS set

Briana Mittleman

9/13/2019