remove lowly expressed genes by selecting genes that had FPKM > 0

Question

[ATCG]

Hi, I have to remove lowly expressed genes by selecting genes that had FPKM > 0 in at least 90% of individuals. How can I do this in R? Also In the following expression, I'm confused what the last part, >= 294 is filtering. table(rowSums(exprs>0)>=294) Thanks!

Answer 1

[ATCG]

Using genefilter library(genefilter)

f1<- kOverA(265, 0) ffun <- filterfun(f1) wh1 <- genefilter(exprs, ffun) sum(wh1) exprs.filt<-exprs[wh1,]

or exprs.filt.2<-exprs[rowSums(exprs>0)>=265,] To confirm that both methods keep the same genes table(rownames(exprs.filt)==rownames(exprs.filt.2))