Last updated: 2019-08-30

Checks: 6 1

Knit directory: apaQTL/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). 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: objects present

The global environment had objects present when the code in the R Markdown file was run. These objects 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. Use wflow_publish or wflow_build to ensure that the code is always run in an empty environment.

The following objects were defined in the global environment when these results were created:

Name Class Size
data environment 56 bytes
env environment 56 bytes

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: 80f8466

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:    docs/.DS_Store
    Ignored:    docs/figure/.DS_Store
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  .Rprofile
    Untracked:  ._.DS_Store
    Untracked:  .gitignore
    Untracked:  @
    Untracked:  _workflowr.yml
    Untracked:  analysis/._PASdescriptiveplots.Rmd
    Untracked:  analysis/._cuttoffPercUsage.Rmd
    Untracked:  analysis/QTLexampleplots.Rmd
    Untracked:  analysis/cuttoffPercUsage.Rmd
    Untracked:  analysis/eQTLoverlap.Rmd
    Untracked:  analysis/interpret verify bam.Rmd
    Untracked:  analysis/interpret_verifybam.Rmd
    Untracked:  analysis/mergeRNA.Rmd
    Untracked:  analysis/oldstuffNotNeeded.Rmd
    Untracked:  analysis/totalspec.Rmd
    Untracked:  apaQTL.Rproj
    Untracked:  code/.NascentRNAdtPlotFirstintronicPAS.sh.swp
    Untracked:  code/._ApaQTL_nominalNonnorm.sh
    Untracked:  code/._BothFracDTPlotGeneRegions.sh
    Untracked:  code/._BothFracDTPlotGeneRegions_normalized.sh
    Untracked:  code/._EandPqtl_perm.sh
    Untracked:  code/._EandPqtls.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/._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/._PTTfacetboxplots.R
    Untracked:  code/._PrematureQTLNominal.sh
    Untracked:  code/._PrematureQTLPermuted.sh
    Untracked:  code/._QTL2bed.py
    Untracked:  code/._QTL2bed_withstrand.py
    Untracked:  code/._RNAbam2bw.sh
    Untracked:  code/._RNAseqDTplot.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/._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_nominalv67.sh
    Untracked:  code/._apaQTL_permuted.sh
    Untracked:  code/._apaQTL_permuted_test6A7A.sh
    Untracked:  code/._assignNucIntonpeak2intronlocs.sh
    Untracked:  code/._assignTotIntronpeak2intronlocs.sh
    Untracked:  code/._bam2BW_5primemost.sh
    Untracked:  code/._bed2saf.py
    Untracked:  code/._bothFracDTplot1stintron.sh
    Untracked:  code/._bothFracDTplot4thintron.sh
    Untracked:  code/._bothFrac_FC.sh
    Untracked:  code/._callPeaksYL.py
    Untracked:  code/._changenomQTLres2geneName.py
    Untracked:  code/._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/._extractGenotypes.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/._fixH3k12ac.py
    Untracked:  code/._fixPASregionSNPs.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/._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/._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/._nucQTLGWAS.py
    Untracked:  code/._nucSpecQTLineData.py
    Untracked:  code/._nucSpeceffectsize.py
    Untracked:  code/._pQTLsotherdata.py
    Untracked:  code/._pacbioDT.sh
    Untracked:  code/._pacbioIntronicDT.sh
    Untracked:  code/._parseBestbamid.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/._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_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/._submit-snakemakePAS.sh
    Untracked:  code/._submit-snakemakefiltPAS.sh
    Untracked:  code/._subsetAPAnotEorPgene.py
    Untracked:  code/._subsetAPAnotEorPgene_2versions.py
    Untracked:  code/._subsetApanoteGene.py
    Untracked:  code/._subsetApanoteGene_2versions.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/._testVerifyBam.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_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/ApaQTL_nominalNonnorm.sh
    Untracked:  code/BothFracDTPlot1stintron.err
    Untracked:  code/BothFracDTPlot1stintron.out
    Untracked:  code/BothFracDTPlot4stintron.err
    Untracked:  code/BothFracDTPlot4stintron.out
    Untracked:  code/BothFracDTPlotGeneRegions.err
    Untracked:  code/BothFracDTPlotGeneRegions.out
    Untracked:  code/BothFracDTPlotGeneRegions_norm.err
    Untracked:  code/BothFracDTPlotGeneRegions_norm.out
    Untracked:  code/BothFracDTPlotGeneRegions_normalized.sh
    Untracked:  code/DistPAS2Sig.py
    Untracked:  code/EandPqtl.err
    Untracked:  code/EandPqtl.out
    Untracked:  code/EandPqtl_perm.sh
    Untracked:  code/EandPqtls.sh
    Untracked:  code/EncodeRNADTPlotGeneRegions.err
    Untracked:  code/EncodeRNADTPlotGeneRegions.out
    Untracked:  code/FC_NucintornUpandDown.sh
    Untracked:  code/FC_NucintronPASupandDown.err
    Untracked:  code/FC_NucintronPASupandDown.out
    Untracked:  code/FC_UTR.err
    Untracked:  code/FC_UTR.out
    Untracked:  code/FC_UTR.sh
    Untracked:  code/FC_intornUpandDownsteamPAS.sh
    Untracked:  code/FC_intronPASupandDown.err
    Untracked:  code/FC_intronPASupandDown.out
    Untracked:  code/FC_nascent.err
    Untracked:  code/FC_nascentout
    Untracked:  code/FC_nascentseq.sh
    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/IntronicPASDT.err
    Untracked:  code/IntronicPASDT.out
    Untracked:  code/IntronicPASDT.sh
    Untracked:  code/LC_samplegroups.py
    Untracked:  code/LD_qtl.sh
    Untracked:  code/LD_snpsproxy.sh
    Untracked:  code/LD_vcftools.hap.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/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/NomResfromPASSNP.py
    Untracked:  code/NuclearPAS_5per.bed.py
    Untracked:  code/Nuclear_example.err
    Untracked:  code/Nuclear_example.out
    Untracked:  code/PACbioDT.err
    Untracked:  code/PACbioDT.out
    Untracked:  code/PACbioDTitronic.err
    Untracked:  code/PACbioDTitronic.out
    Untracked:  code/PTTfacetboxplots.R
    Untracked:  code/PrematureQTLNominal.sh
    Untracked:  code/PrematureQTLPermuted.sh
    Untracked:  code/Prematureqtl_nominal.err
    Untracked:  code/Prematureqtl_nominal.out
    Untracked:  code/Prematureqtl_permuted.err
    Untracked:  code/Prematureqtl_permuted.out
    Untracked:  code/QTL2bed.py
    Untracked:  code/QTL2bed_withstrand.py
    Untracked:  code/README.md
    Untracked:  code/RNABam2BW.err
    Untracked:  code/RNABam2BW.out
    Untracked:  code/RNAbam2bw.sh
    Untracked:  code/RNAseqDTPlotGeneRegions.err
    Untracked:  code/RNAseqDTPlotGeneRegions.out
    Untracked:  code/RNAseqDTplot.sh
    Untracked:  code/Rplots.pdf
    Untracked:  code/SAF215upbed.py
    Untracked:  code/Script4NuclearPTTqtlexamples.sh
    Untracked:  code/Script4NuclearQTLexamples.sh
    Untracked:  code/Script4TotalPTTqtlexamples.sh
    Untracked:  code/Script4TotalQTLexamples.sh
    Untracked:  code/TESplots100bp.err
    Untracked:  code/TESplots100bp.out
    Untracked:  code/TESplots100bp.sh
    Untracked:  code/TESplots150bp.err
    Untracked:  code/TESplots150bp.out
    Untracked:  code/TESplots150bp.sh
    Untracked:  code/TESplots200bp.err
    Untracked:  code/TESplots200bp.out
    Untracked:  code/TESplots200bp.sh
    Untracked:  code/TotalPAS_5perc.bed.py
    Untracked:  code/Total_example.err
    Untracked:  code/Total_example.out
    Untracked:  code/Untitled
    Untracked:  code/Upstream100Bases_general.py
    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/ZipandTabPheno.sh
    Untracked:  code/aAPAqtl_nominal39ind.sh
    Untracked:  code/annotatePacBioPASregion.sh
    Untracked:  code/annotatedPAS2bed.py
    Untracked:  code/annotatedPASregion.err
    Untracked:  code/annotatedPASregion.out
    Untracked:  code/apaInPandE.py
    Untracked:  code/apaQTLCorrectPvalMakeQQ_4pc.R
    Untracked:  code/apaQTLCorrectpval_6or7a.R
    Untracked:  code/apaQTL_Nominal_4pc.sh
    Untracked:  code/apaQTL_nominalv67.sh
    Untracked:  code/apaQTL_permuted.4pc.sh
    Untracked:  code/apaQTL_permuted_test6A7A.sh
    Untracked:  code/apafacetboxplots.R
    Untracked:  code/apaqtlfacetboxplots.R
    Untracked:  code/assignNucIntonpeak2intronlocs.sh
    Untracked:  code/assignPeak2Intronicregion.err
    Untracked:  code/assignPeak2Intronicregion.out
    Untracked:  code/assignTotIntronpeak2intronlocs.sh
    Untracked:  code/assigntotPeak2Intronicregion.err
    Untracked:  code/assigntotPeak2Intronicregion.out
    Untracked:  code/bam2BW_5primemost.sh
    Untracked:  code/bam2bw.err
    Untracked:  code/bam2bw.out
    Untracked:  code/bam2bw_5primemost.err
    Untracked:  code/bam2bw_5primemost.out
    Untracked:  code/binary_fileset.log
    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/callSHscripts.txt
    Untracked:  code/changePermQTLres2geneName.py
    Untracked:  code/changenomQTLres2geneName.py
    Untracked:  code/chooseAnno2PAS_pacbio.py
    Untracked:  code/closestannotated.err
    Untracked:  code/closestannotated.out
    Untracked:  code/closestannotated.sh
    Untracked:  code/closestannotated_byfrac.sh
    Untracked:  code/closestannotatedbyfrac.err
    Untracked:  code/closestannotatedbyfrac.out
    Untracked:  code/codingdms2bed.py
    Untracked:  code/convertNominal2SNPLOC.py
    Untracked:  code/convertNominal2SNPloc2Versions.py
    Untracked:  code/correctNomeqtl.R
    Untracked:  code/createPlinkSampfile.py
    Untracked:  code/dag.pdf
    Untracked:  code/dagPAS.pdf
    Untracked:  code/dagfiltPAS.pdf
    Untracked:  code/eQTL_switch2snploc.py
    Untracked:  code/eQTLgenestestedapa.py
    Untracked:  code/encodeRNADTplots.sh
    Untracked:  code/environmentLeaf.yaml
    Untracked:  code/extractGenotypes.py
    Untracked:  code/extractseqfromqtlfastq.py
    Untracked:  code/fc2leafphen.py
    Untracked:  code/fc_filteredPAS6and7As.sh
    Untracked:  code/fifteenBPupstreamPAS.py
    Untracked:  code/fiftyBPupstreamPAS.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/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_short.py
    Untracked:  code/fixFChead_summary.py
    Untracked:  code/fixH3k12ac.py
    Untracked:  code/fixPASregionSNPs.py
    Untracked:  code/fixRNAhead4corr.py
    Untracked:  code/fixRNAkalisto.py
    Untracked:  code/fixgroupedtranscript.py
    Untracked:  code/fixhead_netseqfc.py
    Untracked:  code/genotypesYRI.gen.proc.keep.vcf.log
    Untracked:  code/genotypesYRI.gen.proc.keep.vcf.recode.vcf
    Untracked:  code/get100upPAS.py
    Untracked:  code/getAPAfromanyeQTL.py
    Untracked:  code/getApapval4eqtl.py
    Untracked:  code/getApapval4eqtl_unexp.py
    Untracked:  code/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/getSeq100up.sh
    Untracked:  code/getUpstreamIntronNuclear.py
    Untracked:  code/getseq100up.err
    Untracked:  code/getseq100up.out
    Untracked:  code/grouptranscripts.err
    Untracked:  code/grouptranscripts.out
    Untracked:  code/grouptranscripts.py
    Untracked:  code/intersectPAS_ssSNPS.err
    Untracked:  code/intersectPAS_ssSNPS.out
    Untracked:  code/intersectVCFPAS.err
    Untracked:  code/intersectVCFPAS.out
    Untracked:  code/intersectVCFandupPAS.sh
    Untracked:  code/keep5perMAF.py
    Untracked:  code/keepSNP_vcf.sh
    Untracked:  code/log/
    Untracked:  code/makeSAFbothfrac5perc.py
    Untracked:  code/makeSNP2rsidfile.py
    Untracked:  code/makeeQTLempirical_unexp.py
    Untracked:  code/makeeQTLempiricaldist.py
    Untracked:  code/makegencondeTSSfile.py
    Untracked:  code/mapSSsnps2PAS.sh
    Untracked:  code/mergRNABam.sh
    Untracked:  code/mergeBW_norm.sh
    Untracked:  code/mergeBWnorm.err
    Untracked:  code/mergeBWnorm.out
    Untracked:  code/mergeBamNacent.err
    Untracked:  code/mergeBamNacent.out
    Untracked:  code/mergeBamNascent.sh
    Untracked:  code/mergeRNAbam.err
    Untracked:  code/mergeRNAbam.out
    Untracked:  code/mnase1stintron.sh
    Untracked:  code/mnaseDTPlot1stintron.err
    Untracked:  code/mnaseDTPlot1stintron.out
    Untracked:  code/mnaseDTPlot4thintron.err
    Untracked:  code/mnaseDTPlot4thintron.out
    Untracked:  code/mnaseDT_fourthintron.sh
    Untracked:  code/netDTPlot4thintron.out
    Untracked:  code/netseqDTplot1stIntron.sh
    Untracked:  code/netseqFC.err
    Untracked:  code/netseqFC.out
    Untracked:  code/netseqFC.sh
    Untracked:  code/neyDTPlot4thintron.err
    Untracked:  code/nucQTLGWAS.py
    Untracked:  code/nucQTLGWAS_withLD.py
    Untracked:  code/nucSpecQTLineData.py
    Untracked:  code/nucSpeceffectsize.py
    Untracked:  code/pQTLsotherdata.py
    Untracked:  code/pacbioDT.sh
    Untracked:  code/pacbioIntronicDT.sh
    Untracked:  code/parseBestbamid.py
    Untracked:  code/phenoQTLfromlist.py
    Untracked:  code/plink.log
    Untracked:  code/processYRIgen.py
    Untracked:  code/prxySNP.err
    Untracked:  code/prxySNP.out
    Untracked:  code/pttFacetBoxplots.err
    Untracked:  code/pttFacetBoxplots.out
    Untracked:  code/pttQTLsinapaQTL.py
    Untracked:  code/pullTwoMechData.py
    Untracked:  code/qtlFacetBoxplots.err
    Untracked:  code/qtlFacetBoxplots.out
    Untracked:  code/qtlRegionseq.sh
    Untracked:  code/qtlsPvalOppFrac.py
    Untracked:  code/rLD_vcftools.hap.err
    Untracked:  code/removeXfromHmm.py
    Untracked:  code/removeloc_pheno.py
    Untracked:  code/riboQTL.sh
    Untracked:  code/riboqtl.err
    Untracked:  code/riboqtl.out
    Untracked:  code/runBestBamID.err
    Untracked:  code/runCorrectNomEqtl.sh
    Untracked:  code/runCorrectNomeqtl.err
    Untracked:  code/runCorrectNomeqtl.out
    Untracked:  code/runFilterLD.err
    Untracked:  code/runFilterLD.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_bam2bw.err
    Untracked:  code/run_bam2bw.out
    Untracked:  code/run_bam2bw_all3prime.sh
    Untracked:  code/run_bam2bw_extra3.sh
    Untracked:  code/run_bam2bwexta.err
    Untracked:  code/run_bam2bwexta.out
    Untracked:  code/run_bestbamid.sh
    Untracked:  code/run_distPAS2Sig.sh
    Untracked:  code/run_filtersnpLD.sh
    Untracked:  code/run_getAPAfromanyeQTL.err
    Untracked:  code/run_getAPAfromanyeQTL.out
    Untracked:  code/run_getAPAfromeQTL_version6.7.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_getapafromeQTL.sh
    Untracked:  code/run_getapapval4eqtl_unexp.sh
    Untracked:  code/run_leafcutterDiffIso.sh
    Untracked:  code/run_leafcutter_ds.err
    Untracked:  code/run_leafcutter_ds.out
    Untracked:  code/run_prxySNP.sh
    Untracked:  code/run_pttfacetboxplot.sh
    Untracked:  code/run_qtlFacetBoxplots.sh
    Untracked:  code/run_sepUsagephen.sh
    Untracked:  code/run_sepgenobychrom.err
    Untracked:  code/run_sepgenobychrom.out
    Untracked:  code/run_sepgenobychrom.sh
    Untracked:  code/run_sepusage.err
    Untracked:  code/run_sepusage.out
    Untracked:  code/run_verifybam.err
    Untracked:  code/run_verifybam.out
    Untracked:  code/run_verifybam.sh
    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/run_verifybam_fullVCF.sh
    Untracked:  code/runprxySNP.err
    Untracked:  code/runprxySNP.out
    Untracked:  code/selectNominalPvalues.py
    Untracked:  code/sepUsagePhen.py
    Untracked:  code/sepgenobychrom.py
    Untracked:  code/seqQTLfastq.err
    Untracked:  code/seqQTLfastq.out
    Untracked:  code/seqQTLregion.err
    Untracked:  code/seqQTLregion.out
    Untracked:  code/snakePASlog.out
    Untracked:  code/snakefiltPASlog.out
    Untracked:  code/sortindexRNABam.err
    Untracked:  code/sortindexRNABam.out
    Untracked:  code/sortindexRNAbam.sh
    Untracked:  code/subsetAPAnotEorPgene.py
    Untracked:  code/subsetAPAnotEorPgene_2versions.py
    Untracked:  code/subsetApanoteGene.py
    Untracked:  code/subsetApanoteGene_2versions.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_SS.err
    Untracked:  code/subsetvcf_SS.out
    Untracked:  code/subsetvcf_noSS.err
    Untracked:  code/subsetvcf_noSS.out
    Untracked:  code/subsetvcf_otherreg.sh
    Untracked:  code/subsetvcf_pas.err
    Untracked:  code/subsetvcf_pas.out
    Untracked:  code/subsetvcf_perm.err
    Untracked:  code/subsetvcf_perm.out
    Untracked:  code/subsetvcf_permSS.sh
    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/subtractExons.sh
    Untracked:  code/subtractfiveprimeUTR.sh
    Untracked:  code/tabixSNPS.sh
    Untracked:  code/tabixSNPs.err
    Untracked:  code/tabixSNPs.out
    Untracked:  code/tenBPupstreamPAS.py
    Untracked:  code/testVerifyBam.sh
    Untracked:  code/test_verifybam.err
    Untracked:  code/test_verifybam.out
    Untracked:  code/totSeceffectsize.py
    Untracked:  code/transcriptdm2bed.py
    Untracked:  code/twentyBPupstreamPAS.py
    Untracked:  code/utrdms2saf.py
    Untracked:  code/vcf2bed.py
    Untracked:  code/vcf_keepsnps.err
    Untracked:  code/vcf_keepsnps.out
    Untracked:  code/verifyBam18517N.sh
    Untracked:  code/verifyBam18517T.sh
    Untracked:  code/verifyBam19128N.sh
    Untracked:  code/verifyBam19128T.sh
    Untracked:  code/wrap_verifybam.err
    Untracked:  code/wrap_verifybam.out
    Untracked:  code/wrap_verifybam.sh
    Untracked:  code/wrap_verifybam_full.sh
    Untracked:  code/writeExampleQTLcode.py
    Untracked:  code/writePTTexamplecode.py
    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/Battle_pQTL/
    Untracked:  data/CompareOldandNew/
    Untracked:  data/DTmatrix/
    Untracked:  data/DiffIso/
    Untracked:  data/EncodeRNA/
    Untracked:  data/ExampleQTLPlots/
    Untracked:  data/FlaggedPAS/
    Untracked:  data/GWAS_overlap/
    Untracked:  data/GeuvadisRNA/
    Untracked:  data/HMMqtls/
    Untracked:  data/Li_eQTLs/
    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_nonNorm/
    Untracked:  data/README.md
    Untracked:  data/RNAseq/
    Untracked:  data/Reads2UTR/
    Untracked:  data/SNPinSS/
    Untracked:  data/SignalSiteFiles/
    Untracked:  data/TF_motifdisruption/
    Untracked:  data/ThirtyNineIndQtl_nominal/
    Untracked:  data/Version15bp6As/
    Untracked:  data/Version15bp7As/
    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/
    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/locusZoom/
    Untracked:  data/mergedBG/
    Untracked:  data/mergedBW_byfrac/
    Untracked:  data/mergedBW_norm/
    Untracked:  data/mergedBam/
    Untracked:  data/mergedbyFracBam/
    Untracked:  data/molPhenos/
    Untracked:  data/molQTLs/
    Untracked:  data/motifdistrupt/
    Untracked:  data/netseq/
    Untracked:  data/nonNorm_pheno/
    Untracked:  data/nuc_10up/
    Untracked:  data/nuc_10upclean/
    Untracked:  data/overlapeQTL_try2/
    Untracked:  data/overlapeQTLs/
    Untracked:  data/pQTLoverlap/
    Untracked:  data/pacbio/
    Untracked:  data/peakCoverage/
    Untracked:  data/peaks_5perc/
    Untracked:  data/phenotype/
    Untracked:  data/phenotype_5perc/
    Untracked:  data/pttQTL/
    Untracked:  data/pttQTLplots/
    Untracked:  data/sigDiffGenes.txt
    Untracked:  data/sort/
    Untracked:  data/sort_clean/
    Untracked:  data/sort_waspfilter/
    Untracked:  data/twoMech/
    Untracked:  data/verifyBAM/
    Untracked:  data/verifyBAM_full/
    Untracked:  docs/._.DS_Store
    Untracked:  docs/figure/._.DS_Store
    Untracked:  docs/figure/nonNormQTL.Rmd/._figure2D-1.pdf
    Untracked:  nohup.out
    Untracked:  output/._.DS_Store
    Untracked:  output/._meanCorrelationPhenotypes.svg
    Untracked:  output/dtPlots/
    Untracked:  output/fastqc/
    Untracked:  output/meanCorrelationPhenotypes.svg
    Untracked:  run_verifybam517N.err
    Untracked:  run_verifybam517N.out

Unstaged changes:
    Modified:   analysis/NuclearSpecAPAqtl.Rmd
    Modified:   analysis/PAS_graphs.Rmd
    Modified:   analysis/PrematureTermQTL.Rmd
    Modified:   analysis/compareAnnotatedpas.Rmd
    Modified:   analysis/overlapapaqtlsandeqtls.Rmd
    Modified:   analysis/rerunQTL_changePC.Rmd
    Modified:   analysis/version15bpfilter.Rmd
    Modified:   code/BothFracDTPlotGeneRegions.sh
    Modified:   code/Snakefile
    Modified:   code/apaQTLCorrectPvalMakeQQ.R
    Modified:   code/apaQTL_Nominal.sh
    Modified:   code/apaQTL_permuted.sh
    Modified:   code/apaQTLsnake.err
    Modified:   code/bam2bw.sh
    Modified:   code/bed2saf.py
    Modified:   code/cluster.json
    Modified:   code/clusterfiltPAS.json
    Modified:   code/config.yaml
    Modified:   code/environment.yaml
    Modified:   code/makePheno.py
    Modified:   code/mergeAllBam.sh
    Modified:   code/mergeByFracBam.sh
    Modified:   code/mergePeaks.sh
    Modified:   code/peakFC.sh
    Modified:   code/snakemake.batch
    Modified:   code/snakemakePAS.batch
    Modified:   code/snakemakefiltPAS.batch
    Modified:   code/submit-snakemake.sh
    Modified:   code/submit-snakemakePAS.sh
    Modified:   code/submit-snakemakefiltPAS.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 1d8fbcb brimittleman 2019-08-29 Build site.
Rmd a6705c8 brimittleman 2019-08-29 add effect size corr for nuc specific
html 2fb467b brimittleman 2019-07-07 Build site.
Rmd bd5f228 brimittleman 2019-07-07 add nuc spec eqtl res

I want to make a qq plot for the eQTL results then seperate the values by genes with a nuclear specific apaQTL.

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 1.4.0
Run ?workflowr for help getting started

First i need to run the permutations on the eQTL data to get the top snp gene associations.

sbatch EandPqtl_perm.sh
cat ../data/molQTLs/fastqtl_qqnorm_RNAseq_phase2.fixed.perm.chunk* > ../data/molQTLs/fastqtl_qqnorm_RNAseq_phase2.fixed.perm.AllNomRes.txt

python changePermQTLres2geneName.py
permeqtl=read.table("../data/molQTLs/fastqtl_qqnorm_RNAseq_phase2.fixed.perm.AllNomRes.GeneName.txt", col.names = c("gene", "nvar","shape1", "shape2", "dummy", "RSID", "dist","nomPval","slope","ppval", "bpval"),stringsAsFactors = F)

permeqtl$bh=p.adjust(permeqtl$bpval, method="fdr")
qqplot(-log10(runif(nrow(permeqtl))), -log10(permeqtl$bpval),ylab="-log10 expression permuted pvalue", xlab="Uniform expectation", main="eQTL")
abline(0,1)

Version Author Date
2fb467b brimittleman 2019-07-07

Seperate for genes with a nuclear specific apaQTL

nuclear specific (only tested in nuclear) are in ../data/QTLoverlap_nonNorm/NuclearSpecQTLinNuclearNominal_nonNorm.txt

nuclear specific not sig in total:

nucSpecgene=read.table("../data/QTLoverlap_nonNorm/NuclearSpecQTLinNuclearNominal_nonNorm.txt",header = F, stringsAsFactors = F, col.names=c("peakID", "snp", "dist", "pval", "Originalslope")) %>% separate(peakID,into=c("gene","loc", "strand", "PAS"),sep="_") %>% select(gene) %>% unique()

nucAPAinTot=read.table("../data/QTLoverlap/NuclearQTLinTotalNominal.txt", header = F, stringsAsFactors = F, col.names=c("peakID", "snp", "dist", "pval", "slope")) %>% separate(peakID,into=c("chr", "start", "end", "geneID"),sep=":" ) %>% separate(geneID, into=c("gene", "loc", "strand", "peakNum"), sep="_")
nucAPAinTot_NOTSIG=nucAPAinTot %>% filter(pval>.05) %>% select(gene) %>% unique()

allNucspec=nucAPAinTot_NOTSIG %>% full_join(nucSpecgene,by="gene")

There are 172 genes in this set.

permeqtl_nucSpec= permeqtl  %>% filter(gene %in%allNucspec$gene )

permeqtl_notnucSpec= permeqtl  %>% anti_join(permeqtl_nucSpec,by = c("gene", "nvar", "shape1", "shape2", "dummy", "RSID", "dist", "nomPval", "slope", "ppval", "bpval", "bh"))
qqplot(-log10(runif(nrow(permeqtl_notnucSpec))), -log10(permeqtl_notnucSpec$bpval),ylab="-log10 expression permuted pvalue", xlab="Uniform expectation", main="eQTL")
points(sort(-log10(runif(nrow(permeqtl_nucSpec)))), sort(-log10(permeqtl_nucSpec$bpval)),col= alpha("Red"))

abline(0,1)
legend("topleft", legend=c("Nuclear specific apaQTL genes", "All other genes"),col=c("red", "black"), pch=16,bty = 'n')

Version Author Date
1d8fbcb brimittleman 2019-08-29
2fb467b brimittleman 2019-07-07 
wilcox.test(permeqtl_notnucSpec$ppval,permeqtl_nucSpec$ppval)

    Wilcoxon rank sum test with continuity correction

data:  permeqtl_notnucSpec$ppval and permeqtl_nucSpec$ppval
W = 194420, p-value = 0.1278
alternative hypothesis: true location shift is not equal to 0

Compare effect sizes:

#allNucspec is the nuclear specific gene, will pull these genes out 

nuclearQTLs=read.table("../data/apaQTLs/Nuclear_apaQTLs_5fdr.txt", header = T,stringsAsFactors = F) %>% rename("gene"= Gene) %>% semi_join(allNucspec, by="gene")

write.table(nuclearQTLs, file="../data/apaQTLs/NuclearSpecificAPAqtls.txt", col.names = T, row.names = F, quote = F, sep="\t")
python nucSpecQTLineData.py

Join these by snp and gene.

nomNamesE=c("gene", "sid",'dist', 'pval', 'Eslope' )
eQTLforNucspec=read.table("../data/eQTLs/NuclearSPecificAPAqtlsinEqtl.txt",stringsAsFactors = F, col.names = nomNamesE)

bothNucspecandE=eQTLforNucspec %>% inner_join(nuclearQTLs, by=c("gene", "sid"))

summary(lm(bothNucspecandE$slope~bothNucspecandE$Eslope))

Call:
lm(formula = bothNucspecandE$slope ~ bothNucspecandE$Eslope)

Residuals:
    Min      1Q  Median      3Q     Max 
-2.8866 -1.0886  0.4571  0.7981  2.2386 

Coefficients:
                       Estimate Std. Error t value Pr(>|t|)    
(Intercept)             0.38684    0.07066   5.475 1.15e-07 ***
bothNucspecandE$Eslope -0.11181    0.23729  -0.471    0.638    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.071 on 228 degrees of freedom
Multiple R-squared:  0.0009729, Adjusted R-squared:  -0.003409 
F-statistic: 0.222 on 1 and 228 DF,  p-value: 0.6379
cor.test(bothNucspecandE$slope,bothNucspecandE$Eslope, alternative="less")

    Pearson's product-moment correlation

data:  bothNucspecandE$slope and bothNucspecandE$Eslope
t = -0.4712, df = 228, p-value = 0.319
alternative hypothesis: true correlation is less than 0
95 percent confidence interval:
 -1.00000000  0.07781426
sample estimates:
        cor 
-0.03119076 
ggplot(bothNucspecandE, aes(x=Eslope, y=slope)) + geom_point() + geom_smooth(method="lm") + labs(x="eQTL effect size", y="apaQTL effect size", title="Effect size in eQTL for nuclear specific apaQTL")

Version Author Date
1d8fbcb brimittleman 2019-08-29 

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_1.4.0 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 plyr_1.8.4       compiler_3.5.1  
 [5] pillar_1.3.1     git2r_0.25.2     highr_0.7        tools_3.5.1     
 [9] digest_0.6.18    lubridate_1.7.4  jsonlite_1.6     evaluate_0.12   
[13] nlme_3.1-137     gtable_0.2.0     lattice_0.20-38  pkgconfig_2.0.2 
[17] rlang_0.4.0      cli_1.1.0        rstudioapi_0.10  yaml_2.2.0      
[21] haven_1.1.2      withr_2.1.2      xml2_1.2.0       httr_1.3.1      
[25] knitr_1.20       hms_0.4.2        generics_0.0.2   fs_1.3.1        
[29] rprojroot_1.3-2  grid_3.5.1       tidyselect_0.2.5 glue_1.3.0      
[33] R6_2.3.0         readxl_1.1.0     rmarkdown_1.10   modelr_0.1.2    
[37] magrittr_1.5     whisker_0.3-2    backports_1.1.2  scales_1.0.0    
[41] htmltools_0.3.6  rvest_0.3.2      assertthat_0.2.0 colorspace_1.3-2
[45] labeling_0.3     stringi_1.2.4    lazyeval_0.2.1   munsell_0.5.0   
[49] broom_0.5.1      crayon_1.3.4