SnpAnnotationDataFrame {GWASTools} | R Documentation

## Class SnpAnotationDataFrame

### Description

The SnpAnnotationDataFrame class stores annotation data associated with SNPs, as well as metadata describing each column. It extends the `AnnotatedDataFrame` class.

### Extends

`AnnotatedDataFrame`

### Constructor

  `SnpAnnotationDataFrame(data, metadata)`:

  `data` must be a data.frame containing the SNP annotation. It must contain at least the following columns:

  - "snpID": integer vector containing unique SNP ids.

  - "chromosome": integer vector containing chromosome codes.

  - "position": integer vector containing position (in base pairs) on the chromosome.

  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`.

  `metadata` is an optional data.frame containing a description for each column in `data`. It should contain a column "labelDescription", with `row.names(metadata) == names(data)`.

  The `SnpAnnotationDataFrame` constructor creates and returns a SnpAnnotationDataFrame instance.

### Accessors

In the code snippets below, `object` is a SnpAnnotationDataFrame object.

  `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.

  `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.

  `getVariable(object, varname, index)`: A vector of the column `varname`. The optional `index` is a logical or integer vector specifying elements to extract. If `varname` is itself a vector, returns a data.frame. Returns `NULL` if `varname` is not found in `object`.

  `hasVariable(object, varname)`: Returns `TRUE` if `varname` is a column in `object`, `FALSE` if not.

  `getVariableNames(object)`: Returns a character vector with the names of all columns in `object`.

  `getAnnotation(object)`: Returns all annotation variables as a data frame.

  `getMetadata(object)`: Returns metadata describing the annotation variables as a data frame.

Inherited methods from `AnnotatedDataFrame`:

  `varLabels(object)`: Returns a character vector with the names of all columns in `object`.

  `pData(object)`: Returns all annotation variables as a data frame, or sets the annotation variables with `pData(object) <- df`.

  `varMetadata(object)`: Returns metadata describing the annotation variables as a data frame, or sets the metadata with `varMetadata(object) <- df`.

  The operators `[`, `$`, and `[[` work just as they do in standard data frames, for both retrieval and assignment.

  `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

`AnnotatedDataFrame`, `ScanAnnotationDataFrame`, `GenotypeData`, `IntensityData`

### Examples

    library(GWASdata)
    data(illumina_snp_annot)
    snpAnnot <- SnpAnnotationDataFrame(illumina_snp_annot)

    # list columns
    varLabels(snpAnnot)

    # add metadata
    meta <- varMetadata(snpAnnot)
    meta["snpID", "labelDescription"] <- "unique integer ID"
    varMetadata(snpAnnot) <- meta

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

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

    # get rsID
    if (hasVariable(snpAnnot, "rsID")) rsID <- getVariable(snpAnnot, "rsID")

    # display data
    head(pData(snpAnnot))

    # standard operators
    snpID <- snpAnnot$snpID
    chrom <- snpAnnot[["chromosome"]]
    subset <- snpAnnot[1:10, 1:5]
    snpAnnot$newVar <- rep(1, nrow(snpAnnot))

    # replace data
    df <- pData(snpAnnot)
    pData(snpAnnot) <- df

    # PLINK chromosome coding
    snpID <- 1:10
    chrom <- c(rep(1L,5), 23:27)
    pos <- 101:110
    df <- data.frame(snpID=snpID, chromosome=chrom, position=pos)
    snpAnnot <- SnpAnnotationDataFrame(df, YchromCode=24L, XYchromCode=25L)
    getChromosome(snpAnnot, char=TRUE)

[Package GWASTools version 1.36.0 Index]