IntensityData-class {GWASTools} | 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

### See Also

`SnpAnnotationDataFrame`, `SnpAnnotationSQLite`, `ScanAnnotationDataFrame`, `ScanAnnotationSQLite`, `ScanAnnotationDataFrame`, `GdsIntensityReader`, `NcdfIntensityReader`, `GenotypeData`

### 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)

[Package GWASTools version 1.40.0 Index]