Compute PCA, no plots

Compute PCA, no plots

Usage

PCA_calc(
  experiment = c("SWATH", "TMT"),
  data,
  scaleR = FALSE,
  scaleC = TRUE,
  k = min(dim(data)) - 2
)

Arguments

experiment

experiment: either SWATH or TMT

data

The prot.ag dataframe. Long format intensity? data with protein name as first column.

scaleR

TO BE DETERMINED - leave as FALSE as on GenePattern - manual row scaling?

scaleC

Pass scaling argument to prcomp function for PCA. Default TRUE.

k

Number of components to compute. Defaults to number of variables - 1.

Value

The components of the PCA that are labelled for easy plotting