GenotypeData-class: Class GenotypeData
In smgogarten/GWASTools: Tools for Genome Wide Association Studies

GenotypeData-class

R Documentation

Class GenotypeData

Description

The GenotypeData class is a container for storing genotype data from a genome-wide association study together with the metadata associated with the subjects and SNPs involved in the study.

Details

The GenotypeData class consists of three slots: data, snp annotation, and scan annotation. There may be multiple scans associated with a subject (e.g. duplicate scans for quality control), hence the use of "scan" as one dimension of the data. Snp and scan annotation are optional, but if included in the GenotypeData object, their unique integer ids (snpID and scanID) are checked against the ids stored in the data slot to ensure consistency.

Constructor

GenotypeData(data, snpAnnot=NULL, scanAnnot=NULL):

data must be an NcdfGenotypeReader, GdsGenotypeReader, or MatrixGenotypeReader object.

snpAnnot, if not NULL, must be a SnpAnnotationDataFrame or SnpAnnotationSQLite object.

scanAnnot, if not NULL, must be a ScanAnnotationDataFrame or ScanAnnotationSQLite object.

The GenotypeData constructor creates and returns a GenotypeData instance, ensuring that data, snpAnnot, and scanAnnot are internally consistent.

Accessors

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

nsnp(object): The number of SNPs in the data.
nscan(object): The number of scans in the data.
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).
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.
getSex(object, index): A character vector of sex, with values 'M' or 'F'. The optional index is a logical or integer vector specifying elements to extract.
hasSex(object): Returns TRUE if the column 'sex' is present in object.
getGenotype(object, snp=c(1,-1), scan=c(1,-1), char=FALSE, sort=TRUE, 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. If char=TRUE, genotypes are returned as characters of the form "A/B". If sort=TRUE, alleles are lexographically sorted ("G/T" instead of "T/G").
getGenotypeSelection(object, snp=NULL, scan=NULL, snpID=NULL, scanID=NULL, char=FALSE, sort=TRUE, drop=TRUE, use.names=TRUE, ...): May be used only if the data slot contains a GdsGenotypeReader or MatrixGenotypeReader object. 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. Other arguments are identical to getGenotype.
getSnpVariable(object, varname, index): Returns the snp annotation variable varname. The optional index is a logical or integer vector specifying elements to extract.
getSnpVariableNames(object): Returns a character vector with the names of the columns in the snp annotation.
hasSnpVariable(object, varname): Returns TRUE if the variable varname is present in the snp annotation.
getScanVariable(object, varname, index): Returns the scan annotation variable varname. The optional index is a logical or integer vector specifying elements to extract.
getScanVariableNames(object): Returns a character vector with the names of the columns in the scan annotation.
hasScanVariable(object, varname): Returns TRUE if the variable varname is present in the scan annotation.
getVariable(object, varname, drop=TRUE, ...): Extracts the contents of the variable varname from the data. If drop=TRUE, the result is coerced to the lowest possible dimension. Missing values are represented as NA. If the variable is not found, returns NULL.
hasVariable(object, varname): Returns TRUE if the data contains contains varname, FALSE if not.
getSnpAnnotation(object): Returns the snp annotation.
hasSnpAnnotation(object): Returns TRUE if the snp annotation slot is not NULL.
getScanAnnotation(object): Returns the scan annotation.
hasScanAnnotation(object): Returns TRUE if the scan annotation slot is not NULL.
open(object): Opens a connection to the data.
close(object): Closes the data connection.
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

Examples

library(GWASdata)
file <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
gds <- GdsGenotypeReader(file)

# object without annotation
genoData <- GenotypeData(gds)

# object with annotation
data(illuminaSnpADF)
data(illuminaScanADF)
# need to rebuild old SNP annotation object to get allele methods
snpAnnot <- SnpAnnotationDataFrame(pData(illuminaSnpADF))
genoData <- GenotypeData(gds, snpAnnot=snpAnnot, scanAnnot=illuminaScanADF)

# dimensions
nsnp(genoData)
nscan(genoData)

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

# get positions only for chromosome 22
pos22 <- getPosition(genoData, index=(chrom == 22))

# get other annotations
if (hasSex(genoData)) sex <- getSex(genoData)
plate <- getScanVariable(genoData, "plate")
rsID <- getSnpVariable(genoData, "rsID")

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

# starting at snp 100, get 10 snps for the first 5 scans
geno <- getGenotype(genoData, snp=c(100,10), scan=c(1,5))
geno

# return genotypes as "A/B" rather than number of A alleles
geno <- getGenotype(genoData, snp=c(100,10), scan=c(1,5), char=TRUE)
geno

close(genoData)

#--------------------------------------
# An example using a non-human organism
#--------------------------------------
# Chicken has 38 autosomes, Z, and W.  Male is ZZ, female is ZW.
# Define sex chromosomes as X=Z and Y=W.
gdsfile <- tempfile()
simulateGenotypeMatrix(n.snps=10, n.chromosomes=40, n.samples=5,
                       filename=gdsfile, file.type="gds")
gds <- GdsGenotypeReader(gdsfile, autosomeCode=1:38L,
                         XchromCode=39L, YchromCode=40L,
                         XYchromCode=41L, MchromCode=42L)
table(getChromosome(gds))
table(getChromosome(gds, char=TRUE))

# SNP annotation
snpdf <- data.frame(snpID=getSnpID(gds),
                    chromosome=getChromosome(gds),
                    position=getPosition(gds))
snpAnnot <- SnpAnnotationDataFrame(snpdf, autosomeCode=1:38L,
                         XchromCode=39L, YchromCode=40L,
                         XYchromCode=41L, MchromCode=42L)
varMetadata(snpAnnot)[,"labelDescription"] <-
  c("unique integer ID",
    "chromosome coded as 1:38=autosomes, 39=Z, 40=W",
    "base position")

# reverse sex coding to get proper counting of sex chromosome SNPs
scandf <- data.frame(scanID=1:5, sex=c("M","M","F","F","F"),
                     stringsAsFactors=FALSE)
scanAnnot <- ScanAnnotationDataFrame(scandf)
varMetadata(scanAnnot)[,"labelDescription"] <-
  c("unique integer ID",
    "sex coded as M=female and F=male")

genoData <- GenotypeData(gds, snpAnnot=snpAnnot, scanAnnot=scanAnnot)
afreq <- alleleFrequency(genoData)
# frequency of Z chromosome in females ("M") and males ("F")
afreq[snpAnnot$chromosome == 39, c("M","F")]
# frequency of W chromosome in females ("M") and males ("F")
afreq[snpAnnot$chromosome == 40, c("M","F")]

close(genoData)
unlink(gdsfile)

smgogarten/GWASTools documentation built on May 18, 2024, 1:19 a.m.