readGVF: Read CNVs from a .gvf file

Description

Reads CNV data from a .gvf file.

Usage

readGVF(filename)

Arguments

filename

The name of a Genome Variation Format file.

Value

A data frame containing the CNVs. Each row contains the following columns for one CNV:

SampleID: ID assigned to the subject's DNA sample in which the CNV was found
Chr: Chromosome on which the CNV is located
Coord_i: Start position of the CNV on the chromosome
Coord_f: End position of the CNV on the chromosome
Type: CNV type (e.g. "DEL" or "DUP")
Genes: (empty string)
CnvID: ID assigned to the CNV

N.B. that the Genes column is *not* assigned. Normally it should contain genes affected by the CNV -- stored in a delimited format inside a character string (e.g. "54777;255352;84435" for semicolon-delimited EntrezGene identifiers). To assign this column, use the getCnvGenes() function. The data frame can then be assigned to the cnv element of the cnvData list structure that comprises one of the slots in a CnvGSAInput object.

References

http://www.sequenceontology.org/resources/gvf.html

Examples

Run this code

library("cnvGSAdata")
cnvFile <- system.file("extdata", "cnv.gvf", package="cnvGSAdata")
cnv <- readGVF(cnvFile)

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