SortMerlinInputFiles {FEST}R Documentation

Sorting of Merlin input files

Description

Merlin input files are sorted according to chromosome order and increasing genetic map distance in centiMorgans (cM).

Usage

SortMerlinInputFiles(mapfile, datfile, freqfile, pedfile, nNotMarker = 5,
                     prefix = "sorted_", chr = NULL, excludeSNP = NULL)

Arguments

mapfile File of the type filename.map which contains the genetic position of each marker (chromosome and position in cM).
datfile File of the type filename.dat which contains the marker identifiers (e.g. rsIDs).
freqfile File of the type filename.freq which contains the allele frequencies of each marker.
pedfile File of the type filename.ped which contains family information and genotype data for all individuals.
nNotMarker Number of columns in the .ped file that precedes the marker columns (containing genotypes). Default value is 5.
prefix Prefix given to the sorted files. Default is "sorted_".
chr Vector describing the chromosomes to be included, for example c(1:10). Default is NULL (meaning all chromosomes).
excludeSNP Identifiers (e.g. rsIDs) of SNPs that should be excluded. Default is NULL.

Author(s)

Øivind Skare oivind.skare@medisin.uio.no

See Also

ThinMerlinInputFiles

Examples

## The example can not be run, user must supply data.
## Replace "filename" with the name of your files.

## SortMerlinInputFiles("filename.map", "filename.dat", "filename.freq",
##                      "filename.ped", prefix = "sorted_")

[Package FEST version 0.06 Index]