R/bigsnpr-package.R

In privefl/mypack: Analysis of Massive SNP Arrays

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#' @import bigstatsr
#' @useDynLib bigsnpr, .registration = TRUE
#' @importFrom Rcpp sourceCpp
#'
#' @param G A [FBM.code256][FBM.code256-class]
#' (typically `<bigSNP>$genotypes`).\cr
#' **You shouldn't have missing values.** Also, remember to do quality control,
#' e.g. some algorithms in this package won't work if you use SNPs with 0 MAF.
#' @param Gna A [FBM.code256][FBM.code256-class]
#' (typically `<bigSNP>$genotypes`).\cr
#' You can have missing values in these data.
#'
#' @param x A [bigSNP][bigSNP-class].
#'
#' @param infos.chr Vector of integers specifying each SNP's chromosome.\cr
#' Typically `<bigSNP>$map$chromosome`.
#'
#' @param infos.pos Vector of integers specifying the physical position
#' on a chromosome (in base pairs) of each SNP.\cr
#' Typically `<bigSNP>$map$physical.pos`.
#'
#' @param nploidy Number of trials, parameter of the binomial distribution.
#' Default is `2`, which corresponds to diploidy, such as for the human genome.
#'
#' @param ind.row An optional vector of the row indices (individuals) that
#' are used. If not specified, all rows are used.\cr
#' **Don't use negative indices.**
#'
#' @param ind.col An optional vector of the column indices (SNPs) that are used.
#' If not specified, all columns are used.\cr
#' **Don't use negative indices.**
#'
#' @param ncores Number of cores used. Default doesn't use parallelism.
#'   You may use [nb_cores()].
#'
#' @param is.size.in.bp Deprecated.
#'
#' @param obj.bed Object of type [bed], which is the mapping of some bed file.
#'   Use `obj.bed <- bed(bedfile)` to get this object.
#'
#' @keywords internal
"_PACKAGE"

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