transformNormalizeHT12object: Normalize and transform expression sets included in a...

In holgerman/HT12ProcessoR: Preprocessing Illuminas HT12 v4 data

Description

Normalizes and transforms the expression sets included in a HT12prepro object and create additional slots saving the resulting data. See vignette for an example.

Usage

transformNormalizeHT12object(
  ht12object,
  paramfile = NULL,
  normalisation_method = "from_paramfile",
  fn_plot = NULL
)

Arguments

ht12object	A list object of class HT12prepro created with function createExpressionSet()
paramfile	Path to the file specifying parameters
normalisation_method	Method used for normalisation. Either 'quantile' (quantile normalisation) or 'rsn' (robust spline normalisation). If "from_paramfile", than the parameter will be read from the paramfile with the location of this file given in parameter paramfile.
fn_plot	Location where the plot showing normalization and transformation can be saved. If NULL (default), the plot will not be saved

Value

A list object of class HT12prepro including additional slot with an expression set with normalized and transformed data excluding control probe information named '$all_nobkgd_eset_ql' and an additional slot with an expression set with normalized and transformed data including control probe information named '$total_nobkgd_eset_ql' + the slot with the history of the commands named '$history“ is updated

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