createExpressionSet: Create an expressionset from Illumina HT12v4 data

In holgerman/HT12ProcessoR: Preprocessing Illuminas HT12 v4 data

Description

This function loads the expression data from several text files created by Illumina GenomeStudio. These files are specified via the slot $chipsamples of an HT12prepro-object from columns "fileset_id", "nobkgd_f", "con_f",and "sample_f". See vignette for an example.

Usage

createExpressionSet(ht12object, paramfile = NULL,
  colseparator = "from_paramfile")

Arguments

ht12object	A list object of class HT12prepro created with function checkExtractChipsamples()
paramfile	Path to the file specifying parameters
colseparator	Separator splitting numbers into units of 1000. Typically "." or ",". If "from_paramfile", than the parameter will be read from the paramfile with the location of this file given in parameter paramfile.

Value

A list object of class HT12prepro with a slot with updated sample-related attributes of the current processing-stage named '$chipsamples', a slot with the R-object holding expression data used to create the expression set named '$rawdataWOcons_joined', a slot with the R-object holding control data used to create the expression set named '$rawdataOnlycons_joined', a slot with the R-object holding control data used to create the expression set named '$rawdataOnlycons_joined', a slot with expression-set expression data excluding control data named '$all_nobkgd_eset', a slot with expression-set expression data including control data named '$total_nobkgd_eset', a slot with the history of the commands named '$history'including expressionset slots

holgerman/HT12ProcessoR documentation built on Sept. 6, 2018, 1:54 p.m.