GSVA R packages
I’m trying to do a gene set varian analysis using R to detect a specific gene set signature of a specific pathway from 20 samples of RNA-seq. I have this files in BAM format but I don’t know what to do in order to get a panel like this one in the pic!
which R packages are required?
on the Y axis there is the score for a specific singling pathway while the x axis represents the different samples.
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Your best approach would be this:
- produce a raw counts matrix for your BAM files (HT-seq,
featureCounts, or something else)
- normalise the raw counts (EdgeR, DESeq2, etc)
- transform the normalised counts via, e.g., regularised log,
variance stabilisation, or log2 (CPM + 1)
- Run GSVA with the ‘C2’ Broad Institute curated datasets
The output of GSVA will be what you can then use to generate bar plot for each enriched signature / pathway.
I will leave the specifics of each step to you.