Mercurial > repos > fubar > differential_count_models

comparison rgedgeRpaired_nocamera.xml @ 80:335abf087bc5 draft

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author fubar
date Wed, 26 Feb 2014 01:43:53 -0500
parents 17d82de7a2d9
children f86cb6b724ee
comparison
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79:17d82de7a2d9 80:335abf087bc5
592 } 592 }
593 } 593 }
594 print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=','))) 594 print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=',')))
595 print.noquote('Using design matrix:') 595 print.noquote('Using design matrix:')
596 print.noquote(mydesign) 596 print.noquote(mydesign)
597 if (doedgeR) { 597 if (doedgeR == T) {
598 sink('edgeR.log') 598 sink('edgeR.log')
599 #### Setup DGEList object 599 #### Setup DGEList object
600 DGEList = DGEList(counts=workCM, group = group) 600 DGEList = DGEList(counts=workCM, group = group)
601 DGEList = calcNormFactors(DGEList) 601 DGEList = calcNormFactors(DGEList)
602 if (robust_meth == 'ordinary') { 602 if (robust_meth == 'ordinary') {
606 606
607 comdisp = DGEList\$common.dispersion 607 comdisp = DGEList\$common.dispersion
608 estpriorn = getPriorN(DGEList) 608 estpriorn = getPriorN(DGEList)
609 print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F) 609 print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
610 } else { 610 } else {
611 DGEList = estimateGLMRobustDisp(DGEList,design=mydesign, prior.df = edgeR_priordf, maxit = 6, residual.type = robust_meth) 611 DGEList = estimateGLMRobustDisp(DGEList,design=mydesign, prior.df = edgeR_priordf, maxit = 6, residual.type = robust_meth)
612 } 612 }
613 } 613
614
614 DGLM = glmFit(DGEList,design=mydesign) 615 DGLM = glmFit(DGEList,design=mydesign)
615 DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed 616 DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
616 efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors 617 efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
617 normData = (1e+06*DGEList\$counts/efflib) 618 normData = (1e+06*DGEList\$counts/efflib)
618 uoutput = cbind( 619 uoutput = cbind(
816 history_gmt_name = "" 817 history_gmt_name = ""
817 out_edgeR = F 818 out_edgeR = F
818 out_DESeq2 = F 819 out_DESeq2 = F
819 out_VOOM = "$out_VOOM" 820 out_VOOM = "$out_VOOM"
820 edgeR_robust_meth = "ordinary" # control robust deviance options 821 edgeR_robust_meth = "ordinary" # control robust deviance options
821 doDESeq2 = F 822 doDESeq2 = $DESeq2.doDESeq2
822 doVoom = $doVoom 823 doVoom = $doVoom
823 doCamera = F 824 doCamera = F
824 doedgeR = $edgeR.doedgeR 825 doedgeR = $edgeR.doedgeR
825 edgeR_priordf = 10 826 edgeR_priordf = 10
826 827