prep {pcaMethods} | R Documentation

## Pre-process a matrix for PCA

### Description

Scaling and centering a matrix.

### Usage

    prep(object, scale = c("none", "pareto", "vector", "uv"), center = TRUE,
      eps = 1e-12, simple = TRUE, reverse = FALSE, ...)

### Arguments

`object` | Numerical matrix (or an object coercible to such) with samples in rows and variables as columns. Also takes `ExpressionSet` in which case the transposed expression matrix is used.
`scale` | One of "UV" (unit variance a=a/σ_{a}) "vector" (vector normalisation b=b/||b||), "pareto" (sqrt UV) or "none" to indicate which scaling should be used to scale the matrix with a variables and b samples. Can also be a vector of scales which should be used to scale the matrix. `NULL` value is interpreted as `"none"`.
`center` | Either a logical which indicates if the matrix should be mean centred or not, or a vector with averages which should be suntracted from the matrix. `NULL` value is interpreted as `FALSE`
`eps` | Minimum variance, variable with lower variance are not scaled and warning is issued instead.
`simple` | Logical indicating if only the data should be returned or a list with the pre-processing statistics as well.
`reverse` | Logical indicating if matrix should be 'post-processed' instead by multiplying each column with its scale and adding the center. In this case, center and scale should be vectors with the statistics (no warning is issued if not, instead output becomes the same as input).
`...` | Only used for passing through arguments.

### Details

Does basically the same as `scale` but adds some alternative scaling options and functionality for treating pre-processing as part of a model.

### Value

A pre-processed matrix or a list with

`center` | a vector with the estimated centers
`scale` | a vector with the estimated scales
`data` | the pre (or post) processed data

### Author(s)

Henning Redestig

### Examples

    object <- matrix(rnorm(50), nrow=10)
    res <- prep(object, scale="uv", center=TRUE, simple=FALSE)
    obj <- prep(object, scale=res$scale, center=res$center)
    ## same as original
    sum((object - prep(obj, scale=res$scale, center=res$center, rev=TRUE))^2)

[Package pcaMethods version 1.72.0 Index]