R/AllClasses.R

In chr1swallace/annotSnpStats: Annotated SnpMatrix objects

#' Annotated SnpMatrix class
#'
#' SnpMatrix or XSnpMatrix objects, tied to sample and SNP support objects
#'
#' This is a small class to allow subsetting and binding operations to
#' be applied to SnpMatrix objects together with their SNP and sample
#' support objects in single operations.  It means the different
#' objects are assured to always line up.
#'
#'@slot .Data \code{SnpMatrix} or \code{XSnpMatrix} object
#'@slot snps \code{data.frame} with rownames matching colnames of
#'     \code{.Data}
#'@slot samples \code{data.frame} with rownames matching rownames of
#'     \code{.Data}
#'@slot phenotype character giving the column name in samples
#'     representing phenotype
#'@slot alleles character vector of length 2 giving the column names
#'     in snps representing phenotype
#'@slot diploid for aXSnpMatrix logical vector indicating which
#'     samples are from diploid individuals
#' @name aSnpMatrix
#' @rdname aSnpMatrix-class
#' @exportClass aSnpMatrix
#' @author Chris Wallace
setClass("aSnpMatrix",
         representation(snps="data.frame",samples="data.frame",phenotype="character",alleles="character"),
         contains="SnpMatrix",
         validity=function(object) {
           if(ncol(object@.Data) && !identical(rownames(object@snps),colnames(object@.Data)))
             stop("rownames of snps object must exactly match colnames of SnpMatrix object")
           if(nrow(object@.Data) && !identical(rownames(object@samples),rownames(object@.Data)))
             stop("rownames of samples object must exactly match rownames of SnpMatrix object")
           if(length(object@phenotype) && !(object@phenotype %in% colnames(object@samples)))
             stop("phenotype must specify a column name of object@samples")
           if(length(object@alleles) && (!all(object@alleles %in% colnames(object@snps)) ||
                                         length(object@alleles)!=2))
             stop("alleles must specify a two columns of object@snps")
         })

#' @rdname aXSnpMatrix-class
#' @export
setClass("aXSnpMatrix",
         representation(snps="data.frame",samples="data.frame",phenotype="character",alleles="character",dipload="logical"),
         ## should use contains=XSnpMatrix, but bug in snpStats prevents this
         contains="SnpMatrix",
         validity=function(object) {
           if(ncol(object@.Data) && !identical(rownames(object@snps),colnames(object@.Data)))
             stop("rownames of snps object must exactly match colnames of SnpMatrix object")
           if(nrow(object@.Data) && !identical(rownames(object@samples),rownames(object@.Data)))
             stop("rownames of samples object must exactly match rownames of SnpMatrix object")
           if(length(object@phenotype) && !(object@phenotype %in% colnames(object@samples)))
             stop("phenotype must specify a column name of object@samples")
           if(length(object@alleles) && (
                      !all(object@alleles %in% colnames(object@snps)) ||
                      length(object@alleles)!=2))
             stop("alleles must specify a two columns of object@snps")
         })