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

In rnabioco/clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

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
)

rnabioco/clustifyr documentation built on Sept. 2, 2024, 11:12 p.m.