snpStats: write.plink – R documentation

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write.plink

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/

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)

snpStats

SnpMatrix and XSnpMatrix classes and methods

v1.40.0

GPL-3

Authors

David Clayton <dc208@cam.ac.uk>

Initial release

2019-10-08