ApplyGSVA: Apply GSVA Method to a Expression Matrix List

In XSLiuLab/GSVAutils: GSVA and Related Functions for Tumor Immunogenicity Score Project

Description

Apply GSVA Method to a Expression Matrix List

Usage

ApplyGSVA(
  GeneSets,
  group_col,
  gene_col,
  ExprMatList,
  method = c("ssgsea", "gsva", "zscore", "plage"),
  kcdf = c("Gaussian", "Poisson"),
  ...
)

Arguments

GeneSets	a data.frame containing groups and genes.
group_col	the column name for groups.
gene_col	the column name for genes.
ExprMatList	a list of expression matrix represented with tibble. See also GenTibbleList().
method	Method to employ in the estimation of gene-set enrichment scores per sample. By default this is set to gsva (H盲nzelmann et al, 2013) and other options are ssgsea (Barbie et al, 2009), zscore (Lee et al, 2008) or plage (Tomfohr et al, 2005). The latter two standardize first expression profiles into z-scores over the samples and, in the case of zscore, it combines them together as their sum divided by the square-root of the size of the gene set, while in the case of plage they are used to calculate the singular value decomposition (SVD) over the genes in the gene set and use the coefficients of the first right-singular vector as pathway activity profile.
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="gsva". By default, kcdf="Gaussian" which is suitable when input expression values are continuous, such as microarray fluorescent units in logarithmic scale, RNA-seq log-CPMs, log-RPKMs or log-TPMs. When input expression values are integer counts, such as those derived from RNA-seq experiments, then this argument should be set to kcdf="Poisson".
...	other arguments passing to GSVA::gsva()

Value

a result list

Examples

data("example_gsets")
data("example_data")

ExprList <- GenTibbleList(list(example_data))
res <- ApplyGSVA(example_gsets,
  group_col = "Cell_type",
  gene_col = "Symbol", ExprMatList = ExprList, method = "gsva"
)

XSLiuLab/GSVAutils documentation built on Dec. 7, 2019, 12:25 a.m.