visualizePreprocessing: Visualize expression data before and after preprocessing

Description Usage Arguments Value

View source: R/visualizePreprocessing.R

Description

Visualisation of control features and expression data before and after preprocessing in several plots. Thereby, raw data before preprocessing is log2 transformed for a more meaningful comparison

Usage

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visualizePreprocessing(
  ht12object,
  paramfile = NULL,
  show_qcplots_individSamplelevel = "from_paramfile",
  showPlots = T
)

Arguments

ht12object

A list object of class HT12prepro created with function filterAtypicalExpressed()

paramfile

Path to the file specifying parameters

show_qcplots_individSamplelevel

Show QC plots comparing expression values before / after preprocessing either binned on SentrixID ('FALSE') or binned on Sample ID ('TRUE')? If "from_paramfile", than the parameter will be read from the paramfile with the location of this file given in parameter paramfile.

showPlots

Show plots. If FALSE, plots are only stored in slot $dokuobjects_visualizePreprocessing

Value

A list object of class HT12prepro including additional slots $dokuobjects_visualizePreprocessing


holgerman/HT12ProcessoR documentation built on June 5, 2021, 9:18 a.m.