sambar: Main SAMBAR function.

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Main SAMBAR function.

Description

Main SAMBAR function.

Usage

sambar(
  mutdata = mut.ucec,
  esize = exon.size,
  signatureset = system.file("extdata", "h.all.v6.1.symbols.gmt", package = "netZooR",
    mustWork = TRUE),
  cangenes = genes,
  kmin = 2,
  kmax = 4
)

Arguments

mutdata	Mutation data in matrix format. The number of mutations should be listed for samples (rows) and genes (columns).
esize	A integer vector of gene lengths, with gene symbols as names.
signatureset	A file containing gene sets (signatures) in .gmt format. These gene sets will be used to de-sparsify the gene-level mutation scores.
cangenes	A vector of genes, for example of cancer-associated genes. This will be used to subset the gene-level mutation data to.
kmin	The minimum number of subtypes the user wants to assess. Defaults to 2.
kmax	The maximum number of subtypes the user wants to assess. Defaults to 4.

Value

A list of samples and the subtypes to which these samples are assigned, for each k.

Examples

data("exon.size")
data("mut.ucec")
data("genes")
sambar(mutdata=mut.ucec, esize=exon.size, signatureset=system.file("extdata", 
"h.all.v6.1.symbols.gmt", package="netZooR", mustWork=TRUE), 
       cangenes=genes, kmin=2, kmax=4)

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.