calculateSignatures: Calculate single-sample gene set enrichment (ssGSEA) for each...

In dviraran/SingleR: Reference-based single-cell RNA-seq annotation

Description

Calculate single-sample gene set enrichment (ssGSEA) for each single cell

Usage

calculateSignatures(sc_data, species = "Human", signatures = NULL,
  n.break = 1000, numCores = SingleR.numCores)

Arguments

sc_data	the single-cell RNA-seq data set as a matrix with genes as rownames. If the data if from a full-length platform, counts must be normalized to gene length (TPM, RPKM, FPKM, etc.).
species	("Mouse" or "Human")
signatures	a GeneSetCollection object, or NULL to use default signatures
n.break	run ssGSEA for n.break at a time.
numCores	Number of cores to use.

Value

scores for each signature and single cell

dviraran/SingleR documentation built on April 21, 2020, 3:23 p.m.