ThinMerlinInputFiles {FEST}R Documentation

Thinning of Merlin Input files

Description

Merlin input files are thinned based on thresholds for minor allele freqency and minimal distance (in cM) between markers.

Usage

ThinMerlinInputFiles(mapfile, datfile, freqfile, pedfile, nNotMarker = 5,
                     limitCentiMorgan = 0, freqThreshold = 0, suffix = "_thinned")

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 pedfile that precedes the marker columns. Default value equal 5.
limitCentiMorgan The data set is thinned such that the distance between two consecutive markers is larger than this limit. Default value is 0.
freqThreshold Markers with a minor allele frequency smaller or equal to this limit will be removed. Default value is 0.
suffix Suffix that will be added to the filenames of the thinned files.

Author(s)

Øivind Skare oivind.skare@medisin.uio.no

See Also

SortMerlinInputFiles

Examples

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

## nMarkerThinned <- ThinMerlinInputFiles("file.map", "file.dat", "file.freq", "file.ped",
##                                         limitCentiMorgan=0.1, freqThreshold=0.1,
##                                         suffix="_thinned")
## file.rename("file.map_thinned", "file2.map") 
## file.rename("file.dat_thinned", "file2.dat") 
## file.rename("file.freq_thinned", "file2.freq") 
## file.rename("file.ped_thinned", "file2.ped")  

[Package FEST version 0.06 Index]