Description Usage Arguments Value
View source: R/createExpressionSet.R
This function loads the expression data from several text files created by Illumina GenomeStudio. These files are specified via the slot $chipsamples of an HT12prepro-object from columns "fileset_id", "nobkgd_f", "con_f",and "sample_f". See vignette for an example.
1 2 3 4 5 | createExpressionSet(
ht12object,
paramfile = NULL,
colseparator = "from_paramfile"
)
|
ht12object |
A list object of class HT12prepro created with function checkExtractChipsamples() |
paramfile |
Path to the file specifying parameters |
colseparator |
Separator splitting numbers into units of 1000. Typically "." or ",". If "from_paramfile", than the parameter will be read from the paramfile with the location of this file given in parameter paramfile. |
A list object of class HT12prepro with a slot with updated sample-related attributes of the current processing-stage named '$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
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