ssgsea: ssGSEA

In scfurl/m3addon: This package adds to the popular "monocle3"

Description

This function runs ssGSEA as implemented here: https://gist.github.com/gaoce/39e0907146c752c127728ad74e123b33

Usage

ssgsea(X, gene_sets, alpha = 0.25, scale = T, norm = F, single = T)

Arguments

X	matrix. Rows are genes. Columns are samples. Row names are symbols.
gene_sets	list. Each element is a string vector with gene symbols.
alpha	numeric. Parameter for ssGSEA, the default is 0.25
scale	logical. If True, normalize the scores by number of genes in the gene sets.
norm	logical. If True, normalize the scores by the absolute difference between max and min values.
single	logical. If True, use ssGSEA algorithm, otherwise use GSEA.

Value

matrix containing enrichment scroes. Rows are gene sets, columns are samples.

Examples

# Create a fake matrix
m = 100
n = 100
set.seed(1)
X = matrix(rnorm(m*n), m, n)
# Assign 'gene symbols' to row names
rownames(X) = 1:m
# Create 3 gene sets
gene_sets = list(a = sample(m, 5), b = sample(m, 5), c = sample(m, 5))
system.time(assign('a', GSVA::gsva(X, gene_sets, method = 'ssgsea')))
system.time(assign('b', ssgsea(X, gene_sets, scale = F, norm = T)))
identical(a, b)

scfurl/m3addon documentation built on Aug. 9, 2021, 5:30 p.m.