convert.snp.ped {GenABEL} | R Documentation |
Converts genotypic data in pre-makeped linkage fromat (+map) to internal genotypic data formated file
convert.snp.ped(pedfile, mapfile, outfile, bcast = 10000)
pedfile |
Pre-makeped linkage genotypic data file name |
mapfile |
Mega2 map file |
outfile |
Output data file |
bcast |
Reports progress after reading bcast portion of SNPs |
Pedfile must be standard pre-makeped linkage file. In this file, columns are
ped id fa mo sex affection
Sex is coded as 1=male and 2=female. Affection status is not used. For example
1 1 0 0 1 2 1 1 1 2
1 2 0 0 1 0 1 2 1 2
1 3 0 0 2 1 2 2 1 1
Would imply that persons 1, 2 and 3 are "founders" (which would be typical for a case-control study), 1 and 2 are males and 3 is female. Person 1 is homozygous for allele 1 at locus 1 and heterozygous at locus 2. Person 2 is heterozygous at both loci. Person 3 is homozygous for allele 2 at locus 1 and allele 1 at locus 2.
The map file is standard Mega2 map. For example:
chrom kosambi name
18 2859916 rs679153
18 2860891 rs9965482
Says that locus 1 is named rs679153 and located at chromosome 18 position 2859916. Locus 2 (rs9965482) is located at chromosome 18, position 2860891.
Does not return any value
The function does not check if "outfile" already exists, thus it is always over-written
Yurii Aulchenko
load.gwaa.data
,
convert.snp.text
# # convert.snp.ped(ped="pedin.18",map="map.18",out="genos.raw") #