GdsReaderGdsIntensityReader(filename): filename must be the path to a GDS file. The GDS
file must contain the following variables:
autosomeCode,
XchromCode, XYchromCode, YchromCode, and
MchromCode. The GDS file should also contain at least one of the following
variables with dimensions ('snp','sample'):
GdsIntensityReader constructor creates and returns a
GdsIntensityReader instance pointing to this file.
object is a GdsIntensityReader 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.
getScanID(object, index): A unique integer vector of scan
IDs. The optional index is a logical or
integer vector specifying elements to extract.
getQuality(object, snp, scan, drop=TRUE): Extracts quality scores.
The result is a vector or matrix, depending on the number
of dimensions in the returned values and the value of drop. Missing values are
represented as NA.
hasQuality(object):
Returns TRUE if the GDS file contains a variable 'quality'.
getX(object, snp, scan, drop=TRUE): Extracts X intensity.
The result is a vector or matrix, depending on the number
of dimensions in the returned values and the value of drop. Missing values are
represented as NA.
hasX(object):
Returns TRUE if the GDS file contains a variable 'X'.
getY(object, snp, scan, drop=TRUE): Extracts Y intensity.
The result is a vector or matrix, depending on the number
of dimensions in the returned values and the value of drop. Missing values are
represented as NA.
hasY(object):
Returns TRUE if the GDS file contains a variable 'Y'.
getBAlleleFreq(object, snp, scan, drop=TRUE): Extracts B allele frequency.
The result is a vector or matrix, depending on the number
of dimensions in the returned values and the value of drop. Missing values are
represented as NA.
hasBAlleleFreq(object):
Returns TRUE if the GDS file contains a variable 'BAlleleFreq'.
getLogRRatio(object, snp, scan, drop=TRUE): Extracts Log R Ratio.
The result is a vector or matrix, depending on the number
of dimensions in the returned values and the value of drop. Missing values are
represented as NA.
hasLogRRatio(object):
Returns TRUE if the GDS file contains a variable 'LogRRatio'.
getVariable(object, varname, snp, scan, drop=TRUE): Returns the
contents of the variable varname.
The result is a vector or matrix, depending on the number
of dimensions in the returned values and the value of drop. Missing values are
represented as NA. If the variable is not found in the GDS
file, returns NULL.
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.
GdsReader,
GdsGenotypeReader,
GenotypeData, IntensityData
file <- system.file("extdata", "illumina_qxy.gds", package="GWASdata")
gds <- GdsIntensityReader(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
x <- getX(gds, snp=c(1,-1), scan=c(1,1))
# starting at snp 100, get 10 snps for the first 5 scans
x <- getX(gds, snp=c(100,10), scan=c(1,5))
close(gds)
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