edgeR_Notes.txt

A typical edgeR analysis might look like the following. Here we assume there are four
RNA-Seq libraries in two groups, and the counts are stored in a tab-delimited text le, with gene symbols in a column called Symbol.


To perform quasi-likelihood F-tests:
> x <- read.delim("fileofcounts.txt",row.names="Symbol")
> group <- factor(c(1,1,2,2))
> y <- DGEList(counts=x,group=group)
> y <- calcNormFactors(y)
> design <- model.matrix(~group)
> y <- estimateDisp(y,design)
> fit <- glmQLFit(y,design)
> qlf <- glmQLFTest(fit,coef=2)
> topTags(qlf)

#JRT magrittr pipeline
#setup
group <-  factor(exptdesign$ReplicateGroup)
design <- model.matrix(~group)
coef <- length(unique(group))

dgelist <- counts %>% 
	DGEList %>%
	calcNormFactors(method="TMM")      #make method an argument

fit <-	estimateDisp(dgelist, design=design)
	glmQLFit(design=design) 

qlf_toptags  <-  glmQLFTest(fit, coef=coef) %>%
	topTags(n=Inf, sort.by=NULL)

#Return the dgelist, fit and qlf_toptags

#1st look
plotMDS(dgelist, method="bcv")




#specific comparisons
et <- exactTest