GSVA_score_insert: Insert pathway score into the seurat.obj

In Lian-Lab/LIANLAB: To integrate analysis methods and simplify analysis process

Description

Insert pathway score into the seurat.obj

Usage

GSVA_score_insert(
  seurat_object = NULL,
  gspath = NULL,
  species = "mouse",
  min.sz = 2,
  parallel.sz = 12
)

Arguments

seurat_object	it also support a seurat_object instead of expression matrix
gspath	the correct path of your geneset file(.gmt)
species	"mouse"(default),'human'
min.sz	minimum size of the resulting gene sets
parallel.sz	number of threads of execution to use when doing the calculations in parallel

Value

seurat.obj with the score of the pathways

Examples

## Not run: 
input.file <- system.file('extdata','pbmc_1k.RDS',package = 'LIANLABDATA')
pbmc_1k <- readRDS(input.file)
GSVA_pheatmap(pbmc_1k,species="mouse")

## End(Not run)

Lian-Lab/LIANLAB documentation built on June 23, 2021, 5:37 a.m.