runPCA {tomoda} | R Documentation

## Perform PCA

### Description

Perform PCA on sections or genes in a `SummarizedExperiment` object for dimensionality reduction.

### Usage

    runPCA(object, genes = NA, matrix = "auto", scree = FALSE, ...)

### Arguments

`object` | A `SummarizedExperiment` object.
`genes` | `NA` or a vector of character. Perform PCA on sections if it is `NA`, or on given genes if it is a vector of gene names.
`matrix` | Character, must be one of `"auto"`, `"count"`, `"normalized"`, or `"scaled"`. If `"auto"`, normalized matrix is used for sections and scaled matrix is used for genes.
`scree` | Logical, plot the scree plot for PCs if it is `TRUE`.
`...` | Other parameters passed to `prcomp`.

### Value

A `SummarizedExperiment` object. The PC embeddings are saved in slot `meta` if PCA is performed on sections, or saved in slot `gene_embedding` if PCA is performed on genes.

### See Also

`prcomp` for performing PCA on a matrix.

### Examples

    data(zh.data)
    zh <- createTomo(zh.data)

    # Perform PCA on sections.
    zh <- runPCA(zh)

    # Plot the scree plot.
    zh <- runPCA(zh, scree=TRUE)

    # Perform PCA on some genes.
    zh <- runPCA(zh, genes=rownames(zh)[1:100])

[Package tomoda version 1.0.0 Index]