getIC50Matrix: Extract a matrix of IC50 values from a model statistics data...

In CancerRxGene/gdscIC50: Pipeline for GDSC Curve Fitting

Extract a matrix of IC50 values from a model statistics data frame.

Description

Extract a matrix of IC50 values from a model statistics data frame.

Usage

getIC50Matrix(model_stats, drug_identifier = "drug", re_name = T,
  measure = "IC50")

Arguments

model_stats	the results of calcNlmeStats.
drug_identifier	a character vector indicating which column of nlme_stats to use as the "drug" in the IC50matrix. Normally this is the drug column as used in the model fit formula but you may want to change to another identifier for user friendliness e.g. DRUG_ID or DRUG_NAME. The function checks whether there is a one to one mapping between the chosen identifier and the drug column before proceeding. The cell line column is named according to the cl_spec contained in the model_stats.
re_name	logical. Rename the drug columns to GDSCtools standard (Drug_..._IC50). Default is TRUE.
measure	character. Default to "IC50" but can also be set to "auc".

Value

a matrix of IC50s.

See Also

getModelCoef

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")
## Not run: 
nlme_model <- fitModelNlmeData(nlme_data, isLargeData = F)
nlme_stats <- calcNlmeStats(nlme_model, nlme_data)
ic50s <- getIC50Matrix(nlme_stats)
aucs <- getIC50Matrix(nlme_stats, measure = "auc")

## End(Not run)

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