How to keep the genes whose counts are equal or greater than 10
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n_h_78 • 0
@n_h_78-18380
Last seen 2.7 years ago

Hi,

 I wanna keep the genes equal or lower than 10 counts in at least one sample within Deseq2. is the following correct? Doesn't "sum" in "rowSums" indicate adding function?

keep <- rowSums(counts(ddsHTSeq) >= 10) >= 1

 

Thanks in advance,

N. hosseinzadeh

 

deseq2 filtering • 223 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

Yes. You read that from the inside out.

counts(ddsHTSeq) >= 10

returns a boolean matrix with TRUE for any gene with counts >= 10

rowSums() >= 1

computes the number of TRUE values you have, per gene (TRUE/FALSE are coerced to 1/0) and tests that you have >= 1.

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