scgsva: GSVA function for single cell data or data.frame with...

In guokai8/scGSVA: GSVA and UCell signature enrichment analysis for single cell RNA seq

GSVA function for single cell data or data.frame with expression value

Description

GSVA function for single cell data or data.frame with expression value

Usage

scgsva(
  obj,
  annot = NULL,
  assay = NULL,
  slot = "counts",
  batch = 1000,
  method = "ssgsea",
  kcdf = "Poisson",
  abs.ranking = FALSE,
  min.sz = 1,
  max.sz = Inf,
  mx.diff = TRUE,
  ssgsea.norm = TRUE,
  useTerm = TRUE,
  BPPARAM = SnowParam(),
  cores = 4,
  verbose = TRUE,
  sc.keep=TRUE,
  ...
)

Arguments

obj	The count matrix, Seurat, or SingleCellExperiment object.
annot	annotation object
assay	Assay to use in GSVA analysis ('RNA','SCT' or 'Spatial' if spatial transcriptomics)
slot	Specific assay data to get or set
method	to employ in the estimation of gene-set enrichment scores per sample. By default this is set to ssgsea, you can also set it as UCell if you would like use the UCell method
kcdf	Character string denoting the kernel to use during the non-parametric estimation of the cumulative distribution function of expression levels across samples when method="ssgsea". By default, kcdf="Poisson"
abs.ranking	Flag used only when mx.diff=TRUE.
min.sz	Minimum size of the resulting gene sets
max.sz	Maximum size of the resulting gene sets.
mx.diff	Offers two approaches to calculate the enrichment statistic (ES) from the KS random walk statistic.
ssgsea.norm	Logical, set to TRUE (default) with method="ssgsea" runs the SSGSEA method
useTerm	use Term or use id (default: TRUE)
cores	The number of cores to use for parallelization.
sc.keep	keep the whole single cell data or not. Default: TRUE.
verbose	Gives information about each calculation step. Default: FALSE.

Author(s)

Kai Guo

Examples

set.seed(123)
library(scGSVA)
data(pbmc_small)
hsko<-buildAnnot(species="human",keytype="SYMBOL",anntype="KEGG")
res<-scgsva(pbmc_small,hsko)

guokai8/scGSVA documentation built on Nov. 15, 2024, 12:54 a.m.