PCAtools (version 1.3.6)

getVars: getVars

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(). REQUIRED.

components

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

Value

A numeric object.

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)
# }