How edgeR reads an R List object produced by featureCounts
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Gary ▴ 20
Last seen 4.8 years ago

I analyze 20 zebra finch RNA-Seq data, using STAR for alignment, Rsubread-featureCounts for quantification, and edgeR for differentially expressed analysis. However, I don’t know how to run edgeR to read an R List object produced by featureCounts (the detail below). Our study is a three-factor factorial experimental design. I also show the group information below. Could you help me? Many thanks.

Group information

Sample Sex Region Color
Chuong553 Male Cheek Red
Chuong554 Male Head Gray
Chuong555 Female Cheek Gray
Chuong556 Female Head Gray
Chuong557 Male Cheek Red
Chuong558 Male Head Gray
Chuong559 Female Cheek Gray
Chuong560 Female Head Gray
Chuong561 Male Cheek Red
Chuong562 Male Head Gray
Chuong563 Female Cheek Gray
Chuong564 Female Head Gray
Chuong649 Male Cheek Red
Chuong650 Male Cheek Red
Chuong651 Male Cheek Black
Chuong652 Male Cheek Black
Chuong653 Male Cheek White
Chuong654 Male Cheek White
Chuong655 Male Head White
Chuong656 Male Head White


R commands & error messages


edger featurecounts • 1.3k views
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Last seen just now
WEHI, Melbourne, Australia

Feature counts just produces an R object (a simple list) so there is need to read anything. It doesn't write anything to disk. You just use the object directly in your R session, for example

fc <- featureCounts(...)
y <- DGEList(fc$counts)

See for example the section called "Quantifying Read Counts for each Gene" in the edgeR workflow or else the small case study here:

5 Years Later

There is now a new function in the edgeR package to make the conversion easier:

y <- featureCounts2DGEList(fc)

This will extract all the information from the featureCounts output and store it in the appropriate place.

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Thank you so much.


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