BGData: preprocess – R documentation

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preprocess

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)

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.

Value

The centered, scaled, and imputed matrix.

Examples

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

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

BGData

A Suite of Packages for Analysis of Big Genomic Data

v2.2.0

MIT + file LICENSE

Authors

Gustavo de los Campos [aut], Alexander Grueneberg [aut, cre], Paulino Perez [ctb], Ana Vazquez [ctb]

Initial release