MatrixGenotypeReader-class: Class MatrixGenotypeReader

In GWASTools: Tools for Genome Wide Association Studies

Description

The MatrixGenotypeReader class stores a matrix of genotypes as well as SNP and scan IDs, chromosome, and position.

Constructor

MatrixGenotypeReader(genotype=genotype, snpID=snpID, chromosome=chromosome, position=position, scanID=scanID):

genotype must be a matrix with dimensions ('snp','scan') containing the number of A alleles : 2=AA, 1=AB, 0=BB.

snp must be a unique integer vector of SNP ids.

chromosome must be an integer vector of chromosomes. Default values for chromosome codes are 1-22=autosome, 23=X, 24=XY, 25=Y, 26=M. The defaults may be changed with the arguments autosomeCode, XchromCode, XYchromCode, YchromCode, and MchromCode.

position must be an integer vector of base positions

scanID must be a unique integer vector of scan ids .

The MatrixGenotypeReader constructor creates and returns a MatrixGenotypeReader instance.

Accessors

In the code snippets below, object is a MatrixGenotypeReader object.

nsnp(object): The number of SNPs.

nscan(object): The number of scans.

getSnpID(object, index): A unique integer vector of snp IDs. The optional index is a logical or integer vector specifying elements to extract.

getChromosome(object, index, char=FALSE): A vector of chromosomes. The optional index is a logical or integer vector specifying elements to extract. If char=FALSE (default), returns an integer vector. If char=TRUE, returns a character vector with elements in (1:22,X,XY,Y,M,U). "U" stands for "Unknown" and is the value given to any chromosome code not falling in the other categories.

getPosition(object, index): An integer vector of base pair positions. The optional index is a logical or integer vector specifying elements to extract.

getScanID(object, index): A unique integer vector of scan IDs. The optional index is a logical or integer vector specifying elements to extract.

getGenotype(object, snp=c(1,-1), scan=c(1,-1), drop=TRUE, use.names=FALSE): Extracts genotype values (number of A alleles). snp and scan indicate which elements to return along the snp and scan dimensions. They must be integer vectors 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 the entire dimension should be read. If drop=TRUE, the result is coerced to the lowest possible dimension. If use.names=TRUE, names of the resulting vector or matrix are set to the SNP and scan IDs. Missing values are represented as NA.

getGenotypeSelection(object, snp=NULL, scan=NULL, snpID=NULL, scanID=NULL, drop=TRUE, use.names=TRUE): Extracts genotype values (number of A alleles). snp and scan may be integer or logical vectors indicating which elements to return along the snp and scan dimensions. snpID and scanID allow section by values of snpID and scanID. Unlike getGenotype, the values requested need not be in contiguous blocks. If order=="file", genotypes are returned in the order they are stored in the object. If order="selection", the order of SNPs and scans will match the index selection provided in snp and scan respectively. Other arguments are identical to getGenotype.

autosomeCode(object): Returns the integer codes for the autosomes.

XchromCode(object): Returns the integer code for the X chromosome.

XYchromCode(object): Returns the integer code for the pseudoautosomal region.

YchromCode(object): Returns the integer code for the Y chromosome.

MchromCode(object): Returns the integer code for mitochondrial SNPs.

Author(s)

Stephanie Gogarten

See Also

NcdfGenotypeReader, GenotypeData

Examples

snpID <- 1:100
chrom <- rep(1:20, each=5)
pos <- 1001:1100
scanID <- 1:20
geno <- matrix(sample(c(0,1,2,NA), 2000, replace=TRUE), nrow=100, ncol=20)

mgr <- MatrixGenotypeReader(genotype=geno, snpID=snpID,
  chromosome=chrom, position=pos, scanID=scanID)

# dimensions
nsnp(mgr)
nscan(mgr)

# get snpID and chromosome
snpID <- getSnpID(mgr)
chrom <- getChromosome(mgr)

# get positions only for chromosome 10
pos10 <- getPosition(mgr, index=(chrom == 10))

# get all snps for first scan
geno <- getGenotype(mgr, snp=c(1,-1), scan=c(1,1))

# starting at snp 50, get 10 snps for the first 5 scans
geno <- getGenotype(mgr, snp=c(50,10), scan=c(1,5))

GWASTools documentation built on Nov. 8, 2020, 7:49 p.m.