SortMerlinInputFiles {FEST} | R Documentation |
Merlin input files are sorted according to chromosome order and increasing genetic map distance in centiMorgans (cM).
SortMerlinInputFiles(mapfile, datfile, freqfile, pedfile, nNotMarker = 5, prefix = "sorted_", chr = NULL, excludeSNP = NULL)
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).
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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. |
Øivind Skare oivind.skare@medisin.uio.no
## 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_")