calculate_pathway_gsea: Convert expression matrix to GSEA pathway scores (would take...

View source: R/utils.R

calculate_pathway_gseaR Documentation

Convert expression matrix to GSEA pathway scores (would take a similar place in workflow before average_clusters/binarize)

Description

Convert expression matrix to GSEA pathway scores (would take a similar place in workflow before average_clusters/binarize)

Usage

calculate_pathway_gsea(
  mat,
  pathway_list,
  n_perm = 1000,
  scale = TRUE,
  no_warnings = TRUE
)

Arguments

mat

expression matrix

pathway_list

a list of vectors, each named for a specific pathway, or dataframe

n_perm

Number of permutation for fgsea function. Defaults to 1000.

scale

convert expr_mat into zscores prior to running GSEA?, default = FALSE

no_warnings

suppress warnings from gsea ties

Value

matrix of GSEA NES values, cell types as row names, pathways as column names

Examples

gl <- list(
    "n" = c("PPBP", "LYZ", "S100A9"),
    "a" = c("IGLL5", "GNLY", "FTL")
)

pbmc_avg <- average_clusters(
    mat = pbmc_matrix_small,
    metadata = pbmc_meta,
    cluster_col = "classified"
)

calculate_pathway_gsea(
    mat = pbmc_avg,
    pathway_list = gl
)

NCBI-Hackathons/RClusterCT documentation built on July 10, 2022, 6:18 a.m.