mysvd {pathwayPCA} | R Documentation

## Singular Value Decomposition wrapper for supervised PCA

### Description

Center and compute the SVD of a matrix

### Usage

    mysvd(mat, method = svd, n.components = NULL)

### Arguments

`mat` | A matrix of data frame in "tall" format (p \times n).
`method` | What function should be used to extract the left- and right- singular vectors and singular values? Any function that returns the values as a list with components `u`, `v`, and `d` is appropriate. Defaults to `svd`.
`n.components` | How many singular values / vectors to return? Must be an integer less than min(p, n). Best performance increase is for values much less than min(p, n). Defaults to `NULL`.

### Details

The `mysvd` function takes in a tall -Omics data matrix, extracts the feature means, centers the matrix on this mean vector, and calculates the Singular Value Decomposition (SVD) of the centered data matrix. Currently, the SVD is calculated via the `fast.svd` function from `corpcor` package. However, this function calculates all the singular vectors, even when `n.components` is non-`NULL`. We should experiment with other SVD functions, such as the `rsvd` function from the `rsvd` package. ENHANCEMENT.

### Value

A list containing:

- `u` : The first `n.components` left singular vectors of `mat`.

- `d` : The largest `n.component` singular values of `mat`.

- `v` : The first `n.components` right singular vectors of `mat`.

- `feature.means` : A named vector of the feature means of `mat`.

### Examples

      # DO NOT CALL THIS FUNCTION DIRECTLY.
      # Use SuperPCA_pVals() instead

    ## Not run:
      data("colon_pathwayCollection")
      data("colonSurv_df")

      colon_OmicsSurv <- CreateOmics(
        assayData_df = colonSurv_df[,-(2:3)],
        pathwayCollection_ls = colon_pathwayCollection,
        response = colonSurv_df[, 1:3],
        respType = "surv"
      )

      asthmaGenes_char <-
        getTrimPathwayCollection(colon_OmicsSurv)[["KEGG_ASTHMA"]]$IDs

      mysvd(t(getAssay(colon_OmicsSurv))[asthmaGenes_char, ])

    ## End(Not run)

[Package pathwayPCA version 1.10.0 Index]