snp x scan and scan x snp dimensions are supported.
GdsReaderGdsGenotypeReader(filename, genotypeDim): filename must be the path to a GDS file or a gds object.
The GDS file must contain the following variables:
autosomeCode,
XchromCode, XYchromCode, YchromCode, and
MchromCode. The constructor automatically detects whether the GDS file is in snp x scan or scan x snp order using the dimensions of snp.id and sample.id. In the case of GDS files with equal SNP and scan dimensions, genotypeDim is a required input to the function and can take values "snp,scan" or "scan,snp". The GdsGenotypeReader constructor creates and returns a
GdsGenotypeReader instance pointing to this file.
object is a GdsGenotypeReader object.
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 snp
and/or is scan omitted, the entire variable is read. See GdsReader for additional methods. nsnp(object): The number of SNPs in the GDS file.
nscan(object): The number of scans in the GDS file.
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.
getAlleleA(object, index): A character vector of A alleles.
The optional index is a logical or
integer vector specifying elements to extract.
getAlleleB(object, index): A character vector of B alleles.
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, scan, transpose=FALSE): Extracts genotype values
(number of A alleles).
The result is a vector or matrix, depending on the number
of dimensions in the returned values. Missing values are
represented as NA. Genotypes are returned in SNP x scan order if transpose=FALSE, otherwise they are returned in scan x SNP order.
getVariable(object, varname, snp, scan): Extracts the
contents of the variable varname.
The result is a vector or matrix, depending on the number
of dimensions in the returned values. Missing values are
represented as NA. If the variable is not found in the GDS
file, returns NULL.
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.
GdsReader,
GenotypeData
file <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
gds <- GdsGenotypeReader(file)
# dimensions
nsnp(gds)
nscan(gds)
# get snpID and chromosome
snpID <- getSnpID(gds)
chrom <- getChromosome(gds)
# get positions only for chromosome 22
pos22 <- getPosition(gds, index=(chrom == 22))
# get all snps for first scan
geno <- getGenotype(gds, snp=c(1,-1), scan=c(1,1))
# starting at snp 100, get 10 snps for the first 5 scans
geno <- getGenotype(gds, snp=c(100,10), scan=c(1,5))
close(gds)
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