getLoadings: Return component loadings for principal components from an...

In kevinblighe/PCAtools: PCAtools: Everything Principal Components Analysis

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

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().
components	Indices of the principal components whose component loadings will be returned. If NULL, all PC names will be returned.

Details

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

Value

A data.frame object.

Author(s)

Kevin Blighe <[e-mail]>

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)

kevinblighe/PCAtools documentation built on Oct. 22, 2023, 12:01 p.m.