R: function to export GenABEL data in merlin format

export.merlin {GenABEL} | R Documentation

## function to export GenABEL data in merlin format

### Description

Exports GenABEL data to Merlin and other pedigree formats

### Usage

    	export.merlin(data, pedfile = "merlin.ped", datafile = "merlin.dat",
    	     mapfile = "merlin.map", format = "merlin", fixstrand = "no",
    	     extendedmap = TRUE, traits = 1, order = TRUE, stepids = 100,
    	     dpieceFun = "new")

### Arguments

`data` | gwaa.data object
`pedfile` | Output pedigree data file name
`datafile` | Output data (information) file name; no output if NULL
`mapfile` | Output map file name
`format` | Output format, either "merlin" or "plink"
`fixstrand` | "no" – the strand information and coding comes from the data; "+" – change all coding to "+" strand, "-" – change all coding to "-" strand
`extendedmap` | if TRUE extended map (+ strand, + coding) is saved with the name "mapfile.ext", where "mapfile" is the parameter supplied by user
`traits` | How many fake traits to insert before first column of marker data
`order` | Should output be ordered by chromosome and position
`stepids` | make this larger for faster processing and smaller for lower RAM use
`dpieceFun` | function used to dump data. Do use default.

### Details

The use is straightforward, with only the "fixstrand" option requiring some explanation. Consider a SNP on "-" strand with alleles G and A. If this SNP is accessed on "+" strand, the corresponding alleles would be C and T. While for example Affymetrix reports SNPs on bot "+" and "-" strands, HapMap reports coding on "+" strand only. To make data compatible, and/or to run imputations, one will need to convert all SNP codes to "+" strand. This can be achieved by running export.merlin() with fixstrand="+" parameter.

### Value

No value returned; files saved on HDD

### Author(s)

Yurii Aulchenko

### See Also

To load the data to GenABEL again, use `convert.snp.ped`, `load.gwaa.data`.

### Examples

    #
    # load(srdta)
    # export.merlin(srdta[1:50,1:3])
    #

[Package GenABEL version 1.8-0 Index]