Subset count data in DGEList using edgeR/DESeq2
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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
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@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, ].