ptrvListPCA: Runs PCA on a data frame stemming from ptrvReadList()

In ChemoSens/PTRMSR: Analysis of PTRMS data

Runs PCA on a data frame stemming from ptrvReadList()

Description

Runs PCA on a data frame stemming from ptrvReadList()

Usage

ptrvListPCA(
  df,
  ionToRemove = NULL,
  dataType = "productMeans",
  normalizeByEval = FALSE,
  log = FALSE,
  axes = list(c(1, 2)),
  representation = "TwoMaps",
  option = "Correlation",
  variableName = "ion",
  scoreName = "intensity",
  expandBiplot = NULL
)

Arguments

df	data frame with "ion","intensity","product","subject" columns,
ionToRemove	vector of character containing ions to remove from the analysis
dataType	"raw" (if PCA should be computed on the whole dataset) or "productMeans" if PCA should be computed on the product mean table
normalizeByEval	Boolean. By default TRUE.
log	boolean indicated if the intensities should be logged (TRUE) or not (FALSE)
axes	list of couples of integers corresponding to the maps to plot
representation	"twoMaps" or "distanceBiplot"
option	"Correlation" or "Covariance"
variableName	column containing the variable names. Default to 'ion'
scoreName	column name of the score. Default to 'intensity'
expandBiplot	a number corresponding to the expansion of the variables compared to the individuals in the biplot.

ChemoSens/PTRMSR documentation built on June 15, 2025, 10:40 a.m.