mutect: readMutect
In comm03/trysomesigs: Somatic Signatures

Description Usage Arguments Details Value References Examples

Import 'mutect' calls.

1	readMutect(file, columns, strip = FALSE)

`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.

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.

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

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

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