sambar: Main SAMBAR function.

In mararie/SAMBAR: Subtyping Agglomerated Mutations By Annotation Relations

Description

Main SAMBAR function.

Usage

sambar(mutdata = mut.ucec, esize = exon.size,
  signatureset = system.file("extdata", "h.all.v6.1.symbols.gmt", package =
  "SAMBAR", 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).
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.
signature	A file containing gene sets (signatures) in .gmt format. These gene sets will be used to de-sparsify the gene-level mutation scores.
cagenes	A vector of genes, for example of cancer-associated genes. This will be used to subset the gene-level mutation data to.

Value

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

mararie/SAMBAR documentation built on Nov. 23, 2019, 12:36 a.m.