Subset count data in DGEList using edgeR/DESeq2
1
0
Entering edit mode
Fiona • 0
@0f752196
Last seen 2 days ago
United Kingdom

Hello,

I have an enormous methylation dataset (12.6Gb) that is proving too much for my computer to handle. This data is loaded in to R as a DGEList (with counts, samples, genes and a seperate file with experimental metadata), I want to create a subset of count data to use to ensure my analysis code is correct but I am not sure how to do this? I am able to read in the .rds file and look at it but not sure how to take a subset.

When attempting to manipulate the data at all the R session aborts so any help would be greatly appreciated.

edgeR DMR • 56 views
ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 40 minutes ago
WEHI, Melbourne, Australia

DGEList objects subset like matrices. You can subset samples by y[, j] or subset rows by y[i, ].

ADD COMMENT

Login before adding your answer.

Traffic: 398 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6