setConcsForNlme: Adds columns 'maxc' and 'x' to GDSC normalized-data data...

In CancerRxGene/gdscIC50: Pipeline for GDSC Curve Fitting

Adds columns maxc and x to GDSC normalized-data data frame.

Description

This is run prior to running prepNlmeData. The functionality is separate because the resulting 'maxc' column might be used as a 'drug_specifier' in prepNlmeData.

Usage

setConcsForNlme(normalized_data, group_conc_ranges = F,
  conc_col = "CONC")

Arguments

normalized_data	a GDSC normalized-data data frame.
group_conc_ranges	logical. If TRUE then instances where the same drug has been used in different concentration ranges will be grouped together with a single maxc. Default is FALSE.
conc_col	a string to identify the column used for the concentration values - useful for combination drug treatments.

Details

maxc is the maximum micromolar concentration of the treatment drug. x is the conversion of the micromolar screening concentration to a range where the maximum dose = 9

See Also

removeFailedDrugs, removeMissingDrugs, normalizeData, prepNlmeData

Examples

data("gdsc_example")
gdsc_example <- removeFailedDrugs(gdsc_example)
gdsc_example <- removeMissingDrugs(gdsc_example)
gdsc_example <- normalizeData(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.