# prcomp: Principal Components Analysis for "matter" Matrices In matter: A framework for rapid prototyping with file-based data structures

## Description

This method allows computation of a truncated principal components analysis of a `matter_mat` matrix using the implicitly restarted Lanczos method `irlba`.

## Usage

 ```1 2``` ```## S4 method for signature 'matter_mat' prcomp(x, n = 3, retx = TRUE, center = TRUE, scale. = FALSE, ...) ```

## Arguments

 `x` A `matter` matrix. `n` The number of principal componenets to return, must be less than `min(dim(x))`. `retx` A logical value indicating whether the rotated variables should be returned. `center` A logical value indicating whether the variables should be shifted to be zero-centered, or a centering vector of length equal to the number of columns of `x`. The centering is performed implicitly and does not change the out-of-memory data in `x`. `scale.` A logical value indicating whether the variables should be scaled to have unit variance, or a scaling vector of length equal to the number of columns of `x`. The scaling is performed implicitly and does not change the out-of-memory data in `x`. `...` Additional options passed to `irlba`.

## Value

An object of class ‘prcomp’. See `?prcomp` for details.

## Note

The 'tol' truncation argument found in the default `prcomp` method is not supported. In place of the truncation tolerance in the original function, the argument `n` explicitly gives the number of principal components to return. A warning is generated if the argument 'tol' is used.

Kylie A. Bemis

`bigglm`

## Examples

 ```1 2 3 4 5``` ```set.seed(1) x <- matter_mat(rnorm(1000), nrow=100, ncol=10) prcomp(x) ```

### Example output

```Loading required package: biglm

Attaching package: 'matter'

The following objects are masked from 'package:base':

apply, scale

Standard deviations (1, .., p=3):
[1] 1.269363 1.246694 1.187657

Rotation (n x k) = (10 x 3):
PC1         PC2         PC3
[1,]  0.22358717 -0.04384519 -0.03465806
[2,]  0.18511020  0.01905189 -0.02862531
[3,] -0.11992159  0.14134479 -0.54592323
[4,]  0.02046621 -0.40902231 -0.23137567
[5,]  0.72081289  0.07545634 -0.45209190
[6,] -0.23548406 -0.04338255 -0.09948186
[7,]  0.26021110  0.26169750  0.15836329
[8,]  0.49579071 -0.03016529  0.46863222
[9,]  0.10598111 -0.62346748 -0.28297706
[10,]  0.03418671 -0.58715764  0.32765486
```

matter documentation built on Nov. 8, 2020, 6:15 p.m.