DESEQ object filter
1
0
Entering edit mode
Bine ▴ 10
@bine-23912
Last seen 5 weeks ago

Hey guys,

Is this correct? I want to reduce my countData (cts):

The aim is to get at least 8 reads in 20% of the samples (which is 50 samples):

keep<- rowSums(cts>8)>=50

cts <-cts[keep,]

Thank you, Bine

DESeq2 • 147 views
2
Entering edit mode
@kevin
Last seen 2 hours ago

Hi, this is not quite a DESeq2 question, but, nevertheless, yes, this code will return a boolean vector that represents those genes (rows) that have at least 8 read counts in at least 50 samples:

rowSums(cts>=8) >= 50


Kevin

1
Entering edit mode

Thank you very much for confirming!