import.MAF: import.MAF

In TRONCO: TRONCO, an R package for TRanslational ONCOlogy

Description

Import mutation profiles from a Manual Annotation Format (MAF) file. All mutations are aggregated as a unique event type labeled "Mutation" and assigned a color according to the default of function import.genotypes. If this is a TCGA MAF file check for multiple samples per patient is performed and a warning is raised if these occurr. Customized MAF files can be imported as well provided that they have columns Hugo_Symbol, Tumor_Sample_Barcode and Variant_Classification. Custom filters are possible (via filter.fun) to avoid loading the full MAF data. For details and examples regarding the loading functions provided by the package we refer to the Vignette Section 3.

Usage

import.MAF(
  file,
  sep = "\t",
  is.TCGA = TRUE,
  filter.fun = NULL,
  to.TRONCO = TRUE,
  irregular = FALSE,
  paste.to.Hugo_Symbol = NULL,
  merge.mutation.types = TRUE,
  silent = FALSE
)

Arguments

file	MAF filename
sep	MAF separator, default \'\t\'
is.TCGA	TRUE if this MAF is from TCGA; thus its sample codenames can be interpreted
filter.fun	A filter function applied to each row. This is expected to return TRUE/FALSE.
to.TRONCO	If FALSE returns a dataframe with MAF data, not a TRONCO object
irregular	If TRUE seeks only for columns Hugo_Symbol, Tumor_Sample_Barcode and Variant_Classification
paste.to.Hugo_Symbol	If a list of column names, this will be pasted each Hugo_Symbol to yield names such as PHC2.chr1.33116215.33116215
merge.mutation.types	If TRUE, all mutations are considered equivalent, regardless of their Variant_Classification value. Otherwise no.
silent	A parameter to disable/enable verbose messages.

Value

A TRONCO compliant representation of the input MAF

Examples

data(maf)
mutations = import.MAF(maf)
mutations = annotate.description(mutations, 'Example MAF')
mutations = TCGA.shorten.barcodes(mutations)
oncoprint(mutations)

TRONCO documentation built on Nov. 8, 2020, 5:51 p.m.