SnpAnnotationDataFrame-class: Class SnpAnotationDataFrame

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

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)

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