bed_cprodVec: Cross-product with a vector

In bigsnpr: Analysis of Massive SNP Arrays

Cross-product with a vector

Description

Cross-product between a "bed" object and a vector.

Missing values are replaced by 0 (after centering), as if they had been imputed using parameter center.

Usage

bed_cprodVec(
  obj.bed,
  y.row,
  ind.row = rows_along(obj.bed),
  ind.col = cols_along(obj.bed),
  center = rep(0, length(ind.col)),
  scale = rep(1, length(ind.col)),
  ncores = 1
)

Arguments

obj.bed	Object of type bed, which is the mapping of some bed file. Use obj.bed <- bed(bedfile) to get this object.
y.row	A vector of same size as ind.row.
ind.row	An optional vector of the row indices (individuals) that are used. If not specified, all rows are used. Don't use negative indices.
ind.col	An optional vector of the column indices (SNPs) that are used. If not specified, all columns are used. Don't use negative indices.
center	Vector of same length of ind.col to subtract from columns of X.
scale	Vector of same length of ind.col to divide from columns of X.
ncores	Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().

Value

X^T \cdot y.

Examples

bedfile <- system.file("extdata", "example.bed", package = "bigsnpr")
obj.bed <- bed(bedfile)

y.row <- rep(1, nrow(obj.bed))
str(bed_cprodVec(obj.bed, y.row))

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.