pathway_matrices: Create pathway matrices from gene sets

In jackbibby1/SCPA: Single Cell Pathway Analysis

Create pathway matrices from gene sets

Description

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.

Usage

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

## Not run: 
pathway_expression <- pathway_matrices(
     list(sample1, sample2),
     pathways = "your/path_to_gmt",
     sample_names = c("population1", "population2"))

## End(Not run)

jackbibby1/SCPA documentation built on May 14, 2024, 7:16 a.m.