Question

How edgeR reads an R List object produced by featureCounts

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Gary ▴ 20

@gary-7967

Last seen 6.7 years ago

Hi,
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.
Best,
Gary

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
http://68.181.92.180/~Gary/temporal/Rcommend.txt

edger featurecounts • 1.8k views

ADD COMMENT • link updated 2.6 years ago by Gordon Smyth 53k • written 7.4 years ago by Gary ▴ 20

score 2 · Answer 1 · 2018-06-13

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: http://bioinf.wehi.edu.au/RNAseqCaseStudy

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.