loadSNPData: loadSNPData

In bernatgel/FindFocals: Find focal gains & deletions in SNP array data

Description

Loads SNP array data in a tabular format

Usage

loadSNPData(snps.file, genome="hg19", chr.col=NULL, pos.col=NULL, baf.col=NULL, lrr.col=NULL, snp.col=NULL, verbose=TRUE)

Arguments

snps.file	The name of the file with the data
genome	The name of the genome (default to "hg19")
chr.col	The name or number of the column with chromosome information. If NULL, it is automatically identified. (default to NULL)
pos.col	The name or number of the column with position information. If NULL, it is automatically identified. (default to NULL)
baf.col	The name or number of the column with BAF information. If NULL, it is automatically identified. (default to NULL)
lrr.col	The name or number of the column with LRR information. If NULL, it is automatically identified. (default to NULL)
snp.col	The name or number of the column with SNP identifier information. If NULL, it is automatically identified. (default to NULL)
verbose	Wether information messages should be generated. (default to TRUE)

Details

Given a file name, the function loads SNP array data in a tabular format. It will try to identify the columns with the relevant information (chr, position, BAF, LRR, etc...) or will use the column number or name supplied by the user, if any. It will convert the tabular data into a GRanges, with one range per SNP in the table.

Value

A GRanges object with a range per SNP

Note

The returned GRanges will have the chromosome names following the UCSC style irrespective of the original format.

bernatgel/FindFocals documentation built on May 3, 2019, 9:04 p.m.