seekPCA: PCA

In Solatar/seeqR:

Description

Imports: limma

Usage

seekPCA(Counts, Groups, Batches = NA)

Arguments

Counts	matrix oder data.frame with raw counts, Entrez IDs as rownames, and sample names as colnames
Groups	a vector of integers, indicating which column belongs to which group. Must be in the same order as the columns.
Batches	a vector of integers, indicating which column belongs to which batch. Must be in the same order as the columns. Is used to remove batch effects (limma). Note that two batches must have at least one shared group.

Value

A matrix where each row is a sample, and the three columns are principal components

Examples

myCounts
myGroup <- c(1,1,2,1,2,2) #(e.g. you have WT,WT,KO,WT,KO,KO)
myBatch <- c(1,1,1,2,2,2)
myPCA <- seekPCA(myCounts, myGroup, myBatch)

Solatar/seeqR documentation built on Feb. 19, 2021, 8:07 p.m.