Create pathway matrices from gene sets

This function takes a matrix and pathway csv/gmt files and input and creates expression matrices for each pathway. The resulting output is a nested list of expression matrices for each pathway by each sample.

pathway_matrices(samples, pathways, sample_names = NULL)

Arguments

samples

Expression matrix for each population, with each population as a separate list. These matrices can be generated with e.g. SCPA::seurat_extract()

pathways

Either a gene set gmt file, csv file, or output from SCPA::format_pathways() that contains your gene sets of interest. Information on formatting gene sets can be found at https://jackbibby1.github.io/SCPA/articles/using_gene_sets.html.

sample_names

Names of the samples to be used in the output

Examples

if (FALSE) {
pathway_expression <- pathway_matrices(
     list(sample1, sample2),
     pathways = "your/path_to_gmt",
     sample_names = c("population1", "population2"))
}