snpStats: Utilities for snpStats

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

Utilities for snpStats

Description

asSnpMatrix converts a GenotypeData object to a SnpMatrix-class object.

Usage

asSnpMatrix(genoData, snpNames="snpID", scanNames="scanID",
            snp=c(1,-1), scan=c(1,-1))

Arguments

genoData	A GenotypeData object.
snpNames	The name of the SNP variable in genoData to use as the column (SNP) names in the SnpMatrix-class object.
scanNames	The name of the scan variable in genoData to use as the row (scan) names in the SnpMatrix-class object.
snp	An integer vector of the form (start, count), where start is the index of the first data element to read and count is the number of elements to read. A value of '-1' for count indicates that all SNPs should be read.
scan	An integer vector of the form (start, count), where start is the index of the first data element to read and count is the number of elements to read. A value of '-1' for count indicates that all scans should be read.

Details

The default is to extract all SNPs and scans from genoData, but for a large dataset this may exceed R's memory limit. Alternatively, snp and scan may be used to specify (start, count) of SNPs and scans to extract from genoData.

In the SnpMatrix object, genotypes are stored as 0 = missing, 1 = "A/A", 2= "A/B" or "B/A", and 3 = "B/B". (In a GenotypeData object, 0 = "B/B", 1 = "A/B" or "B/A", and 2 = "A/A".) Columns are SNPs with names snpNames and rows are scans with names scanNames (the transpose of the GenotypeData object).

Value

A SnpMatrix-class object.

Author(s)

Stephanie Gogarten

See Also

SnpMatrix-class, GenotypeData

Examples

library(snpStats)
library(GWASdata)
file <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
gds <- GdsGenotypeReader(file)
data(illuminaSnpADF, illuminaScanADF)
genoData <-  GenotypeData(gds, snpAnnot=illuminaSnpADF, scanAnnot=illuminaScanADF)
snpmat <- asSnpMatrix(genoData, snpNames="rsID", scanNames="scanID")
snpmat
as(snpmat[1:5, 1:5], "character")
summary(snpmat)

# only chromosome 21
chr <- getChromosome(genoData)
c21 <- which(chr == 21)
snpmat <- asSnpMatrix(genoData, snpNames="rsID", scanNames="scanID",
                      snp=c(c21[1], length(c21)))
snpmat
close(genoData)

smgogarten/GWASTools documentation built on July 4, 2023, 2:32 a.m.