getComponents {PCAtools} | R Documentation |
Return the principal component labels for an object of class 'pca'.
getComponents( pcaobj, components = NULL)
pcaobj |
Object of class 'pca' created by pca(). REQUIRED. |
components |
Indices of the principal components whose names will be returned. If NULL, all PC names will be returned. DEFAULT = NULL. OPTIONAL. |
A character
object.
Kevin Blighe <kevin@clinicalbioinformatics.co.uk>, Myles Lewis <myles.lewis@qmul.ac.uk>
options(scipen=10) options(digits=6) col <- 20 row <- 20000 mat1 <- matrix( rexp(col*row, rate = 0.1), ncol = col) rownames(mat1) <- paste0('gene', 1:nrow(mat1)) colnames(mat1) <- paste0('sample', 1:ncol(mat1)) mat2 <- matrix( rexp(col*row, rate = 0.1), ncol = col) rownames(mat2) <- paste0('gene', 1:nrow(mat2)) colnames(mat2) <- paste0('sample', (ncol(mat1)+1):(ncol(mat1)+ncol(mat2))) mat <- cbind(mat1, mat2) metadata <- data.frame(row.names = colnames(mat)) metadata$Group <- rep(NA, ncol(mat)) metadata$Group[seq(1,40,2)] <- 'A' metadata$Group[seq(2,40,2)] <- 'B' metadata$CRP <- sample.int(100, size=ncol(mat), replace=TRUE) metadata$ESR <- sample.int(100, size=ncol(mat), replace=TRUE) p <- pca(mat, metadata = metadata, removeVar = 0.1) getComponents(p)