getLoadings {PCAtools}R Documentation

getLoadings

Description

Return component loadings for principal components from an object of class 'pca'.

Usage

getLoadings(
  pcaobj,
  components = NULL)

Arguments

pcaobj

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

components

Indices of the principal components whose component loadings will be returned. If NULL, all PC names will be returned. DEFAULT = NULL. OPTIONAL.

Value

A data.frame object.

Author(s)

Kevin Blighe <kevin@clinicalbioinformatics.co.uk>, Myles Lewis <myles.lewis@qmul.ac.uk>

Examples

  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)

  getLoadings(p)

[Package PCAtools version 1.0.0 Index]