write.plink {snpStats} | R Documentation

## Write files for analysis in the PLINK toolset

### Description

Given a `SnpMatrix` object, together with associated subject and SNP support dataframes, this function writes `.bed`, `.bim`, and `.fam` files for processing in the PLINK toolset

### Usage

    write.plink(file.base, snp.major = TRUE, snps,
       subject.data, pedigree, id, father, mother, sex, phenotype,
       snp.data, chromosome, genetic.distance, position, allele.1, allele.2,
       na.code = 0, human.genome=TRUE)

### Arguments

`file.base` | A character string giving the base filename. The extensions `.bed`, `.bim`, and `.fam` are appended to this string to give the filenames of the three output files
`snp.major` | Logical variable controlling whether the `.bed` file is in SNP-major or subject-major order
`snps` | The `SnpMatrix` or `XSnpMatrix` object to be written out
`subject.data` | (Optional) A subject support dataframe. If supplied, the next six arguments (which define the fields of the PLINK `.fam` file) will be evaluated in this environment, after matching row names with the row names of `snps`. Otherwise they will be evaluated in the calling environment; they then must be of the right length and in the correct order.
`pedigree` | A pedigree (family) identifier. Default is the row names of `snps`.
`id` | An identifier of an individual within family. Default is a vector of `na.code`.
`father` | The within-family identifier of the subject's father. Default is a vector of `na.code`.
`mother` | The within-family identifier of the subject's mother. Default is a vector of `na.code`.
`sex` | Sex of the individual. Default is a vector of `na.code`. This will be coerced to type `numeric`.
`phenotype` | The primary phenotype value. Default is a vector of `na.code`. This will be coerced to type `numeric`.
`snp.data` | (Optional) A SNP support dataframe. If supplied, the next five arguments (which define the columns of the PLINK `.bim` file) will be evaluated in this environment, after matching row names with the column names of `snps`. Otherwise they will be evaluated in the calling environment; they then must be of the right length and in the correct order.
`chromosome` | The chromosome on which the SNP is located. This should either be numeric, as specified by SPLINK, or character, with `"X"`, `"Y"`, `"XY"`, and `"MT"` for the non-numeric values. Default is a vector of `na.code`, or a vector of 23's if `snps` is a `XSnpMatrix`.
`genetic.distance` | The location of the SNP, expressed as a genetic distance. Default is a vector of `na.code`. This will be coerced to type `numeric`.
`position` | The physical location of the SNP, expressed in base pairs. Default is a vector of `na.code`. This will be coerced to type `numeric`.
`allele.1` | A character vector giving the first allele. Default is a vector of `"A"`s.
`allele.2` | A character vector giving the first allele. Default is a vector of `"B"`s.
`na.code` | The code to be written for `NA` in the `.fam` and `.bin` output files. It should be numeric (or capable of coercion to numeric).
`human.genome` | If TRUE, check the `chromosome` argument for valid values.

### Details

For more details of required codings in `.fam` and `.bim` files, see the PLINK documentation.

### Value

Returns `NULL`.

### Author(s)

David Clayton dc208@cam.ac.uk

### References

PLINK: Whole genome association analysis toolset. http://pngu.mgh.harvard.edu/~purcell/plink/

### See Also

`read.plink`, `SnpMatrix-class`, `XSnpMatrix-class`

### Examples

    data(testdata)
    ## the use of as.numeric() below is not necessary since this is done
    ## automatically. It just illustrates use of expressions for these arguments
    ## Note that cc and sex are variables within the subject.data frame
    ## This command writes files test.bed. test.fam and test.bim
    write.plink(file.base="test", snps=Autosomes,
        subject.data=subject.data, phenotype = as.numeric(cc), sex=as.numeric(sex),
        snp.major=FALSE)

[Package snpStats version 1.40.0 Index]