prepNlmeData: Converts GDSC normalized-data data frame to input format for...

In CancerRxGene/gdscIC50: Pipeline for GDSC Curve Fitting

Converts GDSC normalized-data data frame to input format for nlme curve fit.

Description

Converts GDSC normalized-data data frame to input format for nlme curve fit.

Usage

prepNlmeData(normalized_data, cl_id = "",
  drug_specifiers = c("DRUG_ID_lib", "maxc"), include_combos = F)

Arguments

normalized_data	a GDSC normalized-data data frame.
cl_id	spcifies which cell line identifier to be used for nlme input - currently "COSMIC_ID" or "CELL_ID"
drug_specifiers	a character vector containing the names of the columns to be taken from the normalized_data and combined to make the new drug column. The drug column will be used in the nlme model.
include_combos	logical indicating whether or not to include -C tags in the output - you will need to be careful with the drug_specifiers if T, e.g., drug_specifiers = c("SCAN_ID", "lib_drug", "anchor")

Value

data frame with columns DRUG_ID, CELL_LINE_NAME, CL, maxc, x, y, drug, SCAN_ID, norm_neg_pos, drug_spec CL is the cell line identifier. x is the conversion of the micromolar screening concentration to a range where the maximum dose = 9 y is the normalized intensity from the experiment (sometimes called viability) drug a concatenation of the drug_specifier columns (default DRUG_ID and maxc). SCAN_ID The id of the plate scan used to provide the raw data. norm_neg_pos The identifiers of the control tags used to normalise the data separated by '+'. drug_spec the column names used to make the drug column separated by '+'. The original columns will be also included as separate columns.

See Also

removeFailedDrugs, removeMissingDrugs, normalizeData, setConcsForNlme, fitModelNlmeData

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, 
                          cl_id = "COSMIC_ID",
                           drug_specifiers = c("DRUGSET_ID", "lib_drug"))

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