normalizeComboData: normalizeComboData

In CancerRxGene/gdscIC50: Pipeline for GDSC Curve Fitting

normalizeComboData

Description

normalizeComboData returns normalized intensities for the drug treated wells with respect to controls - column normalized_intensity.

Like normalizeData, the TAG column is replaced with lib_drug and dose columns, but also treatment (S or C) , DRUG_ID_anch, CONC_anch and anchor columns. Combination treatments (C) are treated as if the library alone is to be fitted.

Usage

normalizeComboData(myDat, trim = T, neg_control = "NC-1",
  pos_control = "B")

Arguments

myDat	a GDSC raw data data frame.
trim	logical indicating whether to trim normalized values to the range 0 to 1. default (trim = T)
neg_control	The tag used to recognise a negative control well - the upper end of the dynamic range.
pos_control	The tag used to recognise a positive control well - the lower end of the dynamic range.

See Also

removeFailedDrugs, removeMissingDrugs, setConcsForNlme, prepNlmeData

Examples

data("gdsc_example") # Need a combo example here
gdsc_example <- removeFailedDrugs(gdsc_example)
gdsc_example <- removeMissingDrugs(gdsc_example)
gdsc_example <- normalizeComboData(gdsc_example)
gdsc_example <- setConcsForNlme(gdsc_example)
nlme_data <- prepNlmeData(gdsc_example, "COSMIC_ID")

CancerRxGene/gdscIC50 documentation built on Oct. 6, 2022, 2:40 a.m.