R/bigSNP-class.R

In privefl/mypack: Analysis of Massive SNP Arrays

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#' CODE_012: code genotype calls (3) and missing values.
#' @rdname snp_codes
#' @keywords internal
#' @export
CODE_012 <- c(0, 1, 2, rep(NA, 253))

#' CODE_DOSAGE: code genotype calls and missing values (4), and imputed calls (3)
#' and imputed allele dosages rounded to two decimal places (201).
#' @rdname snp_codes
#' @export
CODE_DOSAGE <- c(0, 1, 2, NA, 0, 1, 2, seq(0, 2, by = 0.01), rep(NA, 48))

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#' Class bigSNP
#'
#' An S3 class for representing information on massive SNP arrays.
#'
#' @return A named list with at least 3 slots: \describe{
#'   \item{genotypes}{A [FBM.code256][FBM.code256-class] which is
#'     a special Filebacked Big Matrix encoded with type `raw` (one byte
#'     unsigned integer), representing genotype calls and possibly imputed
#'     allele dosages. Rows are individuals and columns are SNPs.}
#'   \item{fam}{A `data.frame` containing some information on the individuals
#'     (read from a ".fam" file).}
#'   \item{map}{A `data.frame` giving some information on the variants
#'     (read from a ".bim" file).}
#' }
#'
#' @name bigSNP-class
#' @aliases bigSNP-class bigSNP
#' @keywords class
#' @seealso [snp_readBed]
NULL

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