computePCA: Generate PCA

In AbhishekSinha28/tcgaCleaneR: TGCA Data Analysis

Generate PCA

Description

This function is a part of the data analysis functionality of tcgaCleaneR. It performs PCA using SVD algorithm (runSVD()) on the SummarizedExperiment class TCGA Cancer Data across all assays() and generate PCs.

Usage

computePCA(data, nPcs, is.log)

Arguments

data	S4 data object
nPcs	numeric: Number of PCs that needs to be generated
is.log	logical: Checks if the S4 data has log values. If 'False', it converts data to log scale.

Value

A List of S4 class containing n PCs. For all three assays(), two values are returned. sing.val contains singular values with u containing PCs. variation contains the variation of each PC.

Examples

## Not run: 
computePCA(data = brca.data, nPcs = 10, is.log = FALSE)

## End(Not run)

AbhishekSinha28/tcgaCleaneR documentation built on May 6, 2022, 6:46 a.m.