The NcdfGenotypeReader class is an extension of the NcdfReader class
specific to reading genotype data stored in NetCDF files.
Extends
NcdfReader
Constructor
NcdfGenotypeReader(filename):
filename must be the path to a NetCDF file. The NetCDF
file must contain the following variables:
'snp': a coordinate variable with a unique
integer vector of snp ids
'chromosome': integer
chromosome codes of dimension 'snp'
'position': integer position values of dimension 'snp'
'sampleID': a unique integer vector of scan ids with
dimension 'sample'
'genotype':
a matrix of bytes with dimensions ('snp','sample'). The byte values
must be the number of A alleles : 2=AA, 1=AB, 0=BB.
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.
The NcdfGenotypeReader constructor creates and returns a
NcdfGenotypeReader instance pointing to this file.
Accessors
In the code snippets below, object is a NcdfGenotypeReader object.
See NcdfReader for additional methods.
nsnp(object): The number of SNPs in the NetCDF file.
nscan(object): The number of scans in the NetCDF 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.
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 and the result is a matrix, dimnames are set to the SNP and scan IDs.
Missing values are represented as NA.
getVariable(object, varname, ...): Extracts the
contents of the variable varname. If the variable is not found in the NetCDF
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.
file <- system.file("extdata", "illumina_geno.nc", package="GWASdata")
nc <- NcdfGenotypeReader(file)
# dimensions
nsnp(nc)
nscan(nc)
# get snpID and chromosome
snpID <- getSnpID(nc)
chrom <- getChromosome(nc)
# get positions only for chromosome 22
pos22 <- getPosition(nc, index=(chrom == 22))
# get all snps for first scan
geno <- getGenotype(nc, snp=c(1,-1), scan=c(1,1))
# starting at snp 100, get 10 snps for the first 5 scans
geno <- getGenotype(nc, snp=c(100,10), scan=c(1,5))
close(nc)
Results
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> library(GWASTools)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GWASTools/NcdfGenotypeReader-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: NcdfGenotypeReader
> ### Title: Class NcdfGenotypeReader
> ### Aliases: NcdfGenotypeReader-class NcdfGenotypeReader
> ### getVariable,NcdfGenotypeReader-method
> ### getSnpID,NcdfGenotypeReader-method
> ### getChromosome,NcdfGenotypeReader-method
> ### getPosition,NcdfGenotypeReader-method
> ### getScanID,NcdfGenotypeReader-method
> ### getGenotype,NcdfGenotypeReader-method nsnp,NcdfGenotypeReader-method
> ### nscan,NcdfGenotypeReader-method
> ### autosomeCode,NcdfGenotypeReader-method
> ### XchromCode,NcdfGenotypeReader-method
> ### XYchromCode,NcdfGenotypeReader-method
> ### YchromCode,NcdfGenotypeReader-method
> ### MchromCode,NcdfGenotypeReader-method
> ### Keywords: methods classes
>
> ### ** Examples
>
> file <- system.file("extdata", "illumina_geno.nc", package="GWASdata")
> nc <- NcdfGenotypeReader(file)
>
> # dimensions
> nsnp(nc)
[1] 3300
> nscan(nc)
[1] 77
>
> # get snpID and chromosome
> snpID <- getSnpID(nc)
> chrom <- getChromosome(nc)
>
> # get positions only for chromosome 22
> pos22 <- getPosition(nc, index=(chrom == 22))
>
> # get all snps for first scan
> geno <- getGenotype(nc, snp=c(1,-1), scan=c(1,1))
>
> # starting at snp 100, get 10 snps for the first 5 scans
> geno <- getGenotype(nc, snp=c(100,10), scan=c(1,5))
>
> close(nc)
>
>
>
>
>
> dev.off()
null device
1
>