calculate_sig_score_ssgsea: Calculating signature score using ssGSEA method

View source: R/calculate_sig_score.R

calculate_sig_score_ssgseaR Documentation

Calculating signature score using ssGSEA method

Description

Calculating signature score using ssGSEA method

Usage

calculate_sig_score_ssgsea(
  pdata = NULL,
  eset,
  signature,
  mini_gene_count = 3,
  column_of_sample = "ID",
  adjust_eset = FALSE,
  parallel.size = 1L
)

Arguments

pdata

phenotype data of input sample; if phenotype data is NULL, create a data frame with 'Index' and 'ID' contain column names of eset

eset

normalizated transcriptomic data: normalized (CPM, TPM, RPKM, FPKM, etc.)

signature

List of gene signatures

mini_gene_count

filter out signatures with genes less than minimal gene in expression set; default is 5; the minimal gene count for ssGSEA methods should larger than 5 for the robustness of the calculation

column_of_sample

Defines in which column of pdata the sample identifier can be found.

adjust_eset

remove variables with missing value, sd =0, and Inf value

parallel.size

default is 1

Value

data frame with pdata and signature scores for gene sets; signatures in columns, samples in rows

Author(s)

Dongqiang Zeng

Examples

# Loading TCGA-STAD expresion data(raw count matrix)
data("eset_stad", package = "IOBR")
# transform count data to tpm
eset <- count2tpm(eset_stad, idType = "ensembl")
# signature score estimation using ssgsea method
calculate_sig_score_ssgsea(eset = eset, signature = signature_tme)


IOBR/IOBR documentation built on Sept. 9, 2024, 8:36 p.m.