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

IntensityData-class

R Documentation

Class IntensityData

Description

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

Details

The IntensityData 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 IntensityData object, their unique integer ids (snpID and scanID) are checked against the ids stored in the data file to ensure consistency.

Constructor

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

data must be a GdsIntensityReader or NcdfIntensityReader object.

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

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

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

Accessors

In the code snippets below, object is an IntensityData 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.

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.
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.
getQuality(object, snp, scan): Extracts quality scores. The result is a vector or matrix, depending on the number of dimensions in the returned values. Missing values are represented as NA.
getX(object, snp, scan): Extracts X intensity values. The result is a vector or matrix, depending on the number of dimensions in the returned values. Missing values are represented as NA.
getY(object, snp, scan): Extracts Y intensity values. The result is a vector or matrix, depending on the number of dimensions in the returned values. Missing values are represented as NA.
getBAlleleFreq(object, snp, scan): Extracts B allele frequency values. The result is a vector or matrix, depending on the number of dimensions in the returned values. Missing values are represented as NA.
getLogRRatio(object, snp, scan): Extracts Log R Ratio values. The result is a vector or matrix, depending on the number of dimensions in the returned values. Missing values are represented as NA.
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, snp, scan): Extracts the contents of the variable varname from the data. 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, returns NULL.
hasVariable(object, varname): Returns TRUE if the data contains contains varname, FALSE if not.
hasSnpAnnotation(object): Returns TRUE if the snp annotation slot is not NULL.
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_qxy.gds", package="GWASdata")
gds <- GdsIntensityReader(file)

# object without annotation
intenData <- IntensityData(gds)

# object with annotation
data(illuminaSnpADF, illuminaScanADF)
intenData <-  IntensityData(gds, snpAnnot=illuminaSnpADF, scanAnnot=illuminaScanADF)

# dimensions
nsnp(intenData)
nscan(intenData)

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

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

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

# get all snps for first scan
x <- getX(intenData, snp=c(1,-1), scan=c(1,1))

# starting at snp 100, get 10 snps for the first 5 scans
x <- getX(intenData, snp=c(100,10), scan=c(1,5))

close(intenData)

smgogarten/GWASTools documentation built on July 4, 2023, 2:32 a.m.