GenotypeMatrix-class: Class `GenotypeMatrix`

Description

S4 class for storing genotypes efficiently as column-oriented sparse matrices along with variant info

Arguments

Details

This class stores genotypes as a column-oriented sparse numeric matrix, where rows correspond to samples and columns correspond to variants. This is accomplished by extending the dgCMatrix class from which this class inherits all slots. Information about variants is stored in an additional slot named variantInfo. This slot must be of class VariantInfo and have exactly as many elements as the genotype matrix has columns. The variantInfo slot has a dedicated metadata column named MAF that contains the minor allele frequencies (MAFs) of the variants. For convenience, accessor functions variantInfo and MAF are available (see below). Objects of this class should only be created and manipulated by the constructors and accessors described below, as only these methods ensure the integrity of the created objects. Direct modification of object slots is strongly discouraged!

Constructors

See help pages genotypeMatrix and readGenotypeMatrix.

References

http://www.bioinf.jku.at/software/podkat

Examples

Run this code

## create a toy example
A <- matrix(rbinom(50, 2, prob=0.2), 5, 10)
sA <- as(A, "dgCMatrix")
pos <- sort(sample(1:10000, ncol(A)))
seqname <- "chr1"

## variant with 'GRanges' object
gr <- GRanges(seqnames=seqname, ranges=IRanges(start=pos, width=1))
gtm <- genotypeMatrix(A, gr)
gtm
as.matrix(gtm)
variantInfo(gtm)
MAF(gtm)

## variant with 'pos' and 'seqnames' object
genotypeMatrix(sA, pos, seqname)

## variant with 'seqname:pos' strings passed through 'pos' argument
spos <- paste(seqname, pos, sep=":")
spos
genotypeMatrix(sA, spos)

## read data from VCF file using 'readVcf()' from the 'VariantAnnotation'
## package
if (require(VariantAnnotation))
{
    vcfFile <- system.file("examples/example1.vcf.gz", package="podkat")
    sp <- ScanVcfParam(info=NA, genome="GT", fixed=c("ALT", "FILTER"))
    vcf <- readVcf(vcfFile, genome="hgA", param=sp)
    rowRanges(vcf)

    ## call constructor for 'VCF' object
    gtm <- genotypeMatrix(vcf)
    gtm
    variantInfo(gtm)

    ## alternatively, extract information from 'VCF' object and use
    ## variant with character matrix and 'GRanges' positions
    ## note that, in 'VCF' objects, rows correspond to variants and
    ## columns correspond to samples, therefore, we have to transpose the
    ## genotype
    gt <- t(geno(vcf)$GT)
    gt[1:5, 1:5]
    gr <- rowRanges(vcf)
    gtm <- genotypeMatrix(gt, gr)
    as.matrix(gtm[1:20, 1:5, recomputeMAF=TRUE])
}