preprocess {BGData}

Center, scale, and impute data

Description

A faster version of scale with a similar interface that also allows for imputation. The main difference is that this version scales by the standard deviation regardless of whether centering is enabled or not. If centering is enabled, missing values are imputed by 0, otherwise by the mean of the column that contains the value.

Usage

preprocess(X, center = FALSE, scale = FALSE, impute = FALSE,
  nCores = getOption("mc.cores", 2L))

Arguments

X

A numeric matrix.

center

Either a logical value or numeric vector of length equal to the number of columns of X.

scale

Either a logical value or numeric vector of length equal to the number of columns of X.

impute

Indicates whether missing values should be imputed.

nCores

The number of cores (passed to mclapply). Defaults to the number of cores as detected by detectCores.

Value

The centered, scaled, and imputed matrix.

See Also

scale, which this function tries to improve upon.

Examples

# Load example data
bg <- BGData:::loadExample()

# Center and scale genotypes
W <- preprocess(as.matrix(geno(bg)), center = TRUE, scale = TRUE)