Is there a way to sort topTags output for up and down regulated genes separately? i.e. I want the top 20 up regulated and top 20 downregulated:

x <- read.delim("counts.txt",row.names="geneid")

group <- factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2))

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,n=20,sort.by="logFC")

This only gives the upregulated genes. I want the full  table of results, not just a gene list. Is there a way to make sort.by sort up and down? Also is there a way to ouput the toptags table as tab delimited instead of the painful spaced table that is printed?

Thanks very much,

S.

If you want to do some more advanced sorting, I recommend you use n=Inf and then coerce the result to a data frame (using as.data.frame)and perform whatever filtering and sorting you want to. And for writing to a file, look at the documentation for write.table.

n = "all"

Great, thanks. I think n="all" solves this, thanks.

S.