PCA — mR_pca • margheRita

This function allows to perform PCA.

mR_pca(
  mRList = NULL,
  dirout = NULL,
  col_by = "class",
  method = "svd",
  scaling = c("none", "pareto", "vector", "uv"),
  center = TRUE,
  include_QC = TRUE,
  top = Inf,
  nPcs = 2,
  ...
)

Arguments

mRList: mRList object
dirout: output directory
col_by: (default class)
method: see pcaMethods::pca()
scaling: see pcaMethods::prep()
center: whether to center the data or not
include_QC: (default TRUE)
top: only the top most varying features will be used
nPcs: number of principal components
...: further argments to pcaMethods::pca()

Value

mRList object with "pca" element. Images of screeplot and pairs, table of score,loading and variance can be saved if write_output=TRUE.