function to convert genotypic data in pedigree fromat (+map) to internal data format

convert.snp.ped {GenABEL}R Documentation

function to convert genotypic data in pedigree fromat (+map) to internal data format

Description

Converts genotypic data in a variety of pedigree fromats (+map) to internal genotypic data formated file

Usage

convert.snp.ped(pedfile, mapfile, outfile, format = "premakeped", traits = 1, 
	strand = "u", bcast = 10000000, wslash=FALSE, mapHasHeaderLine=TRUE)

Arguments

pedfile Pre-makeped linkage genotypic data file name (no header line)
mapfile Name of the map file (note that by default header line should be included, see 'mapHasHeaderLine' to modify that)
outfile Output data file
format Input data format, either "premakeped" (default, also works with Merlin files), or "mach"
traits How many traits are specified in the pedigree file (usually 1 – affection – or 2 – affection and liability). Has no effect when format = "mach".
strand Specification of strand, one of "u" (unknown), "+", "-" or "file". In the latter case, map-file should contain an extended map (the one including strand and coding)
bcast Reports progress after reading bcast portion of SNPs
wslash Whether alleles are separated with slash (is true for Mach/Merlin format), otherwise it is assumed that alleles are separated with space. When wslash=T it is assumed that genotypes are coded with single characters, separated with slash (no spaces), e.g. "A/G", and not "A/ G" or "A / G".
mapHasHeaderLine Whether map-file has a header line

Details

Pedfile must be standard pre-makeped/Merlin linkage file, or a Mach file. In pre-makeped linkage file, columns are

ped id fa mo sex trait snp1.allele1 snp1.allele2 snp2.allele1 snp2.allele2 ...

For example

1 1 0 0 1 2 A A G T ...

1 2 0 0 1 0 A G T T ...

1 3 0 0 2 1 A A T T ...

...

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.

Only the second and the marker columns are used, thus make sure the IDs are unique!

Accepted allele codes: 1/2, A/B, A/T, A/G, A/C, T/G, T/C, G/C, A/-, T/-, G/-, C/-. Here, "-" stands of a deletion.

The map file is standard Merlin map. For example:

chrom name position

18 rs679153 2859916

18 rs9965482 2860891

Says that locus 1 is named rs679153 and located at chromosome 18 position 2859916. Locus 2 (rs9965482) is located at chromosome 18, position 2860891.

In extended map format, there should be 4th column specifying the strand

chrom name position strand

18 rs679153 2859916 -

18 rs9965482 2860891 +

Accepted strand coding: +, -, u (unknown)

Please note that by default the header line (e.g. "chrom name position") SHOULD be present in your file, though you can use 'mapHasHeaderLine' argument to modify this behavior

Value

Does not return any value, but writes file with GenABEL raw data

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.illumina, convert.snp.mach, convert.snp.text, convert.snp.tped

Examples

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

[Package GenABEL version 1.6-7 Index]