GenomicTools.fileHandler (version 0.1.5.9)

importPED: importPED

Description

Import a PED/MAP file pair

Usage

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

Arguments

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

Value

a pedmap object

Details

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

Examples

# NOT RUN {
 # 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)


# }