snpdata: Class for SNP genotype and phenotype data.

In tobyjohnson/gtx: Genetics ToolboX

Description

Objects of this class contain subject-specific SNP genotype or allele dosage data along with subject-specific phenotypes data, and SNP coded/noncoded allele information.

Usage

is.snpdata(object)
as.snpdata(object)
## S3 method for class 'snpdata'
summary(object, ...)

Arguments

object	an object to test or coerce to snpdata class.
...	other arguments to summary are ignored.

Details

An object of class snpdata is a list with at least two elements, called “snpinfo” and “data”. snpdata$snpinfo must be a data frame with (at least) columns called “snp”, “coded.allele” and “noncoded.allele”. snpdata$data must be a data frame with columns for each SNP in snpdata$snpinfo with column names formed by pasting together the snp and coded.allele with a separating underscore character, e.g. “rs12345_A”.

Author(s)

Toby Johnson [e-mail]

See Also

Widely used formats for measured or imputed SNP genotype data are read by the read.snpdata.plink, read.snpdata.mach and read.snpdata.impute functions, which all return data in the format described above.

Examples

## Not run: 
align.snpdata.coding(params, snpdata)
grs.make.scores(params, snpdata)
grs.onesnp.apply(params, object)
make.moments2(params, phenolist, snpdata)

## End(Not run)

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.