importPED: importPED
In GenomicTools.fileHandler: File Handlers for Genomic Data Analysis

Description Usage Arguments Details Value Author(s) Examples

Import a PED/MAP file pair

1 2	importPED(file, n, snps = NULL, which, split = "\t\| +", sep = ".", na.strings = "0", lex.order = FALSE, verbose = TRUE)

`file`	ped filename
`n`	Number of samples to read
`snps`	map filename
`which`	Names of SNPS to import
`split`	Columns separator in ped file
`sep`	Character that separates Alleles
`na.strings`	Definition for missing values
`lex.order`	Logical, lexicographical order
`verbose`	Logical, verbose output

This function is to a large extend taken from snpStat::read.pedmap, but here is internally the data.table::fread function used that resulted in much faster file processing.

To import the data, the ped file can be provided to the file option and the map file to the snps option. If no option is given to snps and the file option is provided without any file extension, then the ped/map extension are automaticall added

a pedmap object

Daniel Fischer

 # Define here the location on HDD for the example file
   pedPath <- system.file("extdata","example.ped", package="GenomicTools.fileHandler")
   mapPath <- system.file("extdata","example.map", package="GenomicTools.fileHandler")
 # Import the example ped/map files  
   importPED(file=pedPath, snps=mapPath)