TRONCO (version 2.4.2)

import.MAF: import.MAF

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

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)