gaston (version 1.2)

read.bed.matrix: Read a bed.matrix

Description

Create a bed.matrix from a .bed file, and either a .rds file or a .bim and a .fam file.

Usage

read.bed.matrix(basename, bed = paste(basename, ".bed", sep=""), 
                          fam = paste(basename, ".fam", sep=""),
                          bim = paste(basename, ".bim", sep=""), 
                          rds = paste(basename, ".rds", sep=""),
                          verbose = getOption("gaston.verbose",TRUE))

Value

A bed.matrix

Details

If the .rds file exists, the .fam and .bim files will be ignored. To ignore an existing .rds file, set rds = NULL.

The .bed, .fam and .bim files follow the PLINK specifications (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#bed).

If the .bed file does not exist, and basename ends by ".bed", the function will try to generate a new basename by trimming the extension out. This allows to write read.bed.matrix("file.bed") instead of read.bed.matrix("file").

See Also

write.bed.matrix

Examples

# Read RDS and bed files
x <- read.bed.matrix( system.file("extdata", "LCT.bed", package="gaston") )
x