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)