R: function to convert genotypic data in pedigree fromat (+map)...

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 1.8-0 Index]