PCA {scGPS} | R Documentation

## PCA

### Description

Select top variable genes and perform prcomp

### Usage

    PCA(expression.matrix = NULL, ngenes = 1500, scaling = TRUE, npcs = 50)

### Arguments

`expression.matrix` | An expression matrix, with genes in rows
`ngenes` | number of genes used for clustering calculations.
`scaling` | a logical of whether we want to scale the matrix
`npcs` | an integer specifying the number of principal components to use.

### Value

a list containing PCA results and variance explained

### Examples

    day2 <- day_2_cardio_cell_sample
    mixedpop1 <-new_scGPS_object(ExpressionMatrix = day2$dat2_counts,
        GeneMetadata = day2$dat2geneInfo, CellMetadata = day2$dat2_clusters)
    t <-PCA(expression.matrix=assay(mixedpop1))

[Package scGPS version 1.8.0 Index]