Question

Remove genes in a list from cts

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Bine ▴ 50

@bine-23912

Last seen 7 months ago

UK

Dear all,

I hope someone can help me with this as I just cant figure it out. I have my DESEQ2 object cts, which includes all my genes. Now I only want to look at 100 genes, which are in the list "risk_genes".

I tried with cts_new <- cts[cts %in% risk_genes,] but then I am left with 0 genes.

What am I doing wrong?

Thank you so much for any help!!

Bine

DESeq2 • 1.3k views

ADD COMMENT • link updated 3.2 years ago by swbarnes2 ★ 1.4k • written 3.2 years ago by Bine ▴ 50

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That's not the right syntax. Google and experiment until you find the right syntax.

ADD REPLY • link 3.2 years ago swbarnes2 ★ 1.4k

score 1 · Answer 1 · 2021-09-30

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Michael Love 43k

@mikelove

Last seen 17 hours ago

United States

Think about the objects you have. The risk genes is a character vector. If you want to compare to a character vector you need another one. Eg consider rownames()

ADD COMMENT • link 3.2 years ago Michael Love 43k

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I tried different variations now.. I dont know why it is not working..

cts_new<-cts %>% dplyr::filter(rownames(cts) %in% risk_genes_1)

I have been reading in forums and sources but I cant figure it out..

ADD REPLY • link 3.2 years ago Bine ▴ 50

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So you read the DESeq2 vignette? The part about pre-filtering? http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

ADD REPLY • link 3.2 years ago swbarnes2 ★ 1.4k