PCAtools (version 2.5.13)

getVars: Return the explained variation for each principal component for an object of class 'pca'.

Description

Return the explained variation for each principal component for an object of class 'pca'.

Usage

getVars(pcaobj, components = NULL)

Arguments

pcaobj

Object of class 'pca' created by pca().

components

Indices of the principal components whose explained variances will be returned. If NULL, all values will be returned.

Value

A numeric object.

Details

Return the explained variation for each principal component for an object of class 'pca'.

Examples

# NOT RUN {
  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)

  getVars(p)

# }