Fast and reproducible method to downsample a count matrix to different sequencing depths?
Maybe slightly off-topic, moderators please delete if inappropriate.
Could someone recommend a package or function to downsample a count matrix? I'd like to downsample the matrix multiple times so I can test various metrics at different sequencing depths. I'm currently using a downsampling function from the following walkthrough (http://hemberg-lab.github.io/scRNA.seq.course/normalization-for-library-size.html#downsampling), however it can take quite long to carry out and isn't reproducible.
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James Ashmore
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What do you mean by "isn't reproducible"? That different runs will end up in different matrices? If this is the problem, use
set.seed()before running the code.Edit: Sorry yes that's what I mean, so setting the seed should solve that issue.
No I mean if I downsample the matrix to say 1M reads per sample (column), and then I do it again, the downsampling will be slightly different across genes (rows)