[Run GSVA] Run GSVA on gene sets #GSVA #enrichment

run_gsva.R

library("GSVA")
library("fgsea")
library("tidyverse")


# Perform DESeq2 normalization on count data:
dds <- DESeqDataSetFromMatrix(countData = as.matrix(round(counts)), 
                              colData = col_dat, 
                              design = ~ 1)
dds <- estimateSizeFactors(dds)
normalized_counts <- ceiling(counts(dds, normalized=TRUE)-.5)


# Run GSVA:
gsva.es <- gsva(as.matrix(normalized_counts), gs, # gene set collection in a list format
                verbose=T, kcdf="Poisson",        # Gaussian if log-TPM
                method="gsva", parallel.sz = 30)