Fig 1 ARE annotation###################

a.mergePeak2ReadsCounts_V4.2_filteredMergedPeak.R
a.2.normalizePeakCounts.V1.4_H3K27ac.R
a.2.normalizePeakCounts.V1.4_other.R

a_2_peakHeightsNormalized_V1.4/
c.getDiff_byLimma_V1.4.1_sva_NoEHR.R => overall BG peak 

./peakVariationAcrossTiss/
a.mergePeaksAcross3actMarks.R
a.2.extractRefSignalForMergedPeaksFromEpimap_V1.5_HM.R
a.3.identifyAREModulesAcrossEpimap_V1.6.1_merge3ActiveMarks.R
a.4.annotateModuleByrGREAT_3actMarks_Epimap.R
a.pairwiseOvlpPeaks.R


b.annotatePeak.byHomer.R
b.annotatePeak.geneBody.R



Fig 2 ARE differential signal###################




Deconv
a.selectPeakAndSimulation_V1.7.2_colineariyAuto_rowNorm_6Celltypes.R => a_selectPeaksAndSimulation_V1.7.2_colinearAuto_rowNorm_6cellType
b.real.estFract_V1.4.4_nnPoisR_noIntercept_6CellType.R => b_real_estFract_V1.4.4.1_nnPoisR_noIntcpt_peakNorm_6cellType_autoSig
c.cmpDeconvWithEHR_6cellType_V1.1_dTime.R => c_cmpCellFractsWithEHR_6cellType_V1.1_deltaTime

#filter further using the differential peaks background
c.getDiff_byLimma_V1.4.1_sva_NoEHR.R
d.annotateDiffPeak_byrGREAT_V1.4.1_sva_NoEHR.R
d.cmpBulkDPacrossHMs_byLimma_V1.1.R
d.cmpBulkDPacrossHMs_byLimma_V1.2_cmpNumber.R


drug
c.getDiff_byLimma_V1.4_sva.R
d.annotateDiffPeak_byrGREAT_V1.4_sva.R => d_bulkDP_limma_V1.4_annotByrGREAT/ q0.2




evidence for gene body Marks
d.calcHMCorrCrossIndivs_V1.2_promVSgeneBody.R

DEG


#a.geneBodyDP.meta_V1.2_filtByDist.R
genebody signal:  a.geneBodyDP.meta_V1.2.1_allGenes.R
a.2.cmpDPs.geneRegDomainAndGeneBody_V1.1_rmOvlp.R
a.3.visDEG.metaDP_V1.2_5conds.R



Fig 3 genetics###################
a.identifyCovariatesForhaQTL_V1.2.3_filtPeakByMedianCV_geneINT.Peer.R
a.2.callTisshaQTL_V1.2.3_filtPeaksByMedianCV_gINT.Peer_rmSexAge.R
a.3.visHaQTLNumVSCovNum.R
a.4.callTisshaQTL_fixedCov_V1.2.3_dp.bg.R
a.5.multipleTestOnQTL_forPeer_V1.1_cutoffs.R

Peer vs covariates
a.2.testSampPeersWithCovariates.CellFract.R

hQTL vs GWAS: 
a.testBulkHaQTLVSGWAS_byColoc_V1.1_allGWAS.R
a.testBulkHaQTLVSGWAS_byMR_V1.1_allGWAS.R
a.2.BDGWASColocgARE.vs.hQTLSharingWithBrain.R (Fig. S3g)


heritability
a.prepAnnotForLDSC.gARE.R
a.prepAnnotForLDSC.CREGrpAndbulkDP.R
a2.LDSCpartitionHeritab_AREGrp.bulkDP.gCREs_slctGWAS.R
a3.visLDSC_AREGrp.bulkDP.gARE_slctGWAS.R

sharing across HMs
Xushen's method 
b.2.Comp.QTL.DirectionConsistEst.R



Fig 4 causal gene and sharing######################

#linking 
hiC.reg and links: a.buildHiCRegionLink.bulk.R   

differential signal at hiC block level: 	bulk.R =>Screen Shot 2023-04-18 at 4.28.25 PM.png

haQTL vs eQTL coloc: a.2.colocalizeTest.haQTLVSeQTL.coloc_V1.3.gARE_para.R
haQTL vs eQTL MR: a.2.linkGenePeak_MR-Egger_V1.1.1_gARE_para.R
FMeQTL linking: a.linkGenePeak_byFMeQTL_V1.1_gARE.R

genetic linking: 
b.summaryLinks.coloc.MR.PRS_V1.3_gARE.R
b.2.cmp.geneticLinks.vsHiC_V1.1_gARE.R (linkType="gene2Neighb")



candidate genes: based on HiC links with TSS-asscoiated hiC regions, both hQTL-GWAS coloc and differential signal for all histone marks
gene Neigbhood and hic region annotation: a.gneighb.VisGWASANDBulkAnnot_v1.1_bulkLink.R

DP enrichment at HiC block level: a.2.compDPs.hiCBlock.bulk.R
#
candidate genes: based on gLink, both hQTL-GWAS coloc, MR and differential signal, for only H3K4me1, H3K27me3, and H3K27ac
c.gneighb.VisGWASANDBulkAnnot_linkFromGenetics_V1.1_3HM.R

visualization of shared candidate genes from both linking scores
c.2.gneighb.VisGWASANDBulkAnnot_HiCAndgLink.R



compare eQTL Coloc + gLinking/diffPeak
#c.2.cmbPotentialGenes_V1.1_cellsortedeQTL.R
c.2.cmbPotentialGenes_V1.2_bulkAndcellsortedeQTL.R


Fig 5 individual heterogeneity and subtype ###################


b.factorAnalysis.across5HMs.MOFA_HiC.DP_V1.2_pvalCutoff.R
b2.cmpMOFA.Factor.withEHR.R
b3.clusterPatientsBasedOnMOFA.factor.V1.1_allSamps.R

c.cmpPatientClusterWithEHR_byMOFA_V1.1.2_addNumericFeature.R

c.findMarkerDPforCluster_V1.2_uniq.R
c.2.annotateMarkDP_byrGREAT.R