Mercurial > repos > fubar > differential_count_models
changeset 80:335abf087bc5 draft
Uploaded
| author | fubar |
|---|---|
| date | Wed, 26 Feb 2014 01:43:53 -0500 |
| parents | 17d82de7a2d9 |
| children | f86cb6b724ee |
| files | rgedgeRpaired_nocamera.xml |
| diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/rgedgeRpaired_nocamera.xml Wed Feb 26 00:23:05 2014 -0500 +++ b/rgedgeRpaired_nocamera.xml Wed Feb 26 01:43:53 2014 -0500 @@ -594,7 +594,7 @@ print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=','))) print.noquote('Using design matrix:') print.noquote(mydesign) - if (doedgeR) { + if (doedgeR == T) { sink('edgeR.log') #### Setup DGEList object DGEList = DGEList(counts=workCM, group = group) @@ -608,9 +608,10 @@ estpriorn = getPriorN(DGEList) print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F) } else { - DGEList = estimateGLMRobustDisp(DGEList,design=mydesign, prior.df = edgeR_priordf, maxit = 6, residual.type = robust_meth) + DGEList = estimateGLMRobustDisp(DGEList,design=mydesign, prior.df = edgeR_priordf, maxit = 6, residual.type = robust_meth) } - } + + DGLM = glmFit(DGEList,design=mydesign) DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors @@ -818,7 +819,7 @@ out_DESeq2 = F out_VOOM = "$out_VOOM" edgeR_robust_meth = "ordinary" # control robust deviance options -doDESeq2 = F +doDESeq2 = $DESeq2.doDESeq2 doVoom = $doVoom doCamera = F doedgeR = $edgeR.doedgeR