readMutect: readMutect

Description

Import 'mutect' calls.

Usage

readMutect(file, columns, strip = FALSE)

Arguments

file

Location of the mutect tsv files [character, required]

columns

Names of columns to import from the file [character vector, optional, default: missing]. If missing, all columns will be imported.

strip

Should additional columns be imported? [logical, default: FALSE]. If TRUE, return only the bare 'VRanges' object.

Value

A 'VRanges' object, with each row corresponding to one variant in the original file.

Details

The 'readMutect' functions imports the mutational calls of a '*.tsv' file returned by the 'mutect' caller to a 'VRanges' object. For a description of the information of the columns, please refer to the mutect documentation.

References

Cibulskis, Kristian, Michael S. Lawrence, Scott L. Carter, Andrey Sivachenko, David Jaffe, Carrie Sougnez, Stacey Gabriel, Matthew Meyerson, Eric S. Lander, and Gad Getz. "Sensitive Detection of Somatic Point Mutations in Impure and Heterogeneous Cancer Samples." Nature Biotechnology advance online publication (February 10, 2013). doi:10.1038/nbt.2514.

http://www.broadinstitute.org/cancer/cga/mutect_run

Examples

Run this code


mutect_path = system.file("examples", "mutect.tsv", package = "SomaticSignatures")
vr1 = readMutect(mutect_path)
vr2 = readMutect(mutect_path, strip = TRUE)

Run the code above in your browser using DataLab