convert.snp.ped {GenABEL}R Documentation

function to convert genotypic data in pre-makeped linkage fromat (+map) to internal genotypic data formated file

Description

Converts genotypic data in pre-makeped linkage fromat (+map) to internal genotypic data formated file

Usage

convert.snp.ped(pedfile, mapfile, outfile, bcast = 10000)

Arguments

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

Details

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.

Value

Does not return any value

Note

The function does not check if "outfile" already exists, thus it is always over-written

Author(s)

Yurii Aulchenko

See Also

load.gwaa.data, convert.snp.text

Examples

#
# convert.snp.ped(ped="pedin.18",map="map.18",out="genos.raw")
#

[Package GenABEL version 1.1-8 Index]