bed_cprodVec {bigsnpr}

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 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))