ThinMerlinInputFiles {FEST} | R Documentation |
Merlin input files are thinned based on thresholds for minor allele freqency and minimal distance (in cM) between markers.
ThinMerlinInputFiles(mapfile, datfile, freqfile, pedfile, nNotMarker = 5, limitCentiMorgan = 0, freqThreshold = 0, suffix = "_thinned")
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. |
Øivind Skare oivind.skare@medisin.uio.no
## 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")