prepareDrugSets: Prepare drug sets from a table with compound descriptors

In nuno-agostinho/cTRAP: Identification of candidate causal perturbations from differential gene expression data

Prepare drug sets from a table with compound descriptors

Description

Create a list of drug sets for each character and numeric column. For each character column, drugs are split across that column's unique values (see argument maxUniqueElems). For each numeric column, drugs are split across evenly-distributed bins.

Usage

prepareDrugSets(
  table,
  id = 1,
  maxUniqueElems = 15,
  maxBins = 15,
  k = 5,
  minPoints = NULL
)

Arguments

table	Data frame: drug descriptors
id	Integer or character: index or name of the identifier column
maxUniqueElems	Numeric: ignore character columns with more unique elements than maxUniqueElems
maxBins	Numeric: maximum number of bins for numeric columns
k	Numeric: constant; the higher the constant, the smaller the bin size (check minpts)
minPoints	Numeric: minimum number of points in a bin (if NULL, the minimum number of points is the number of non-missing values divided by maxBins divided by k)

Value

Named list of characters: named drug sets with respective compound identifiers as list elements

See Also

Other functions for drug set enrichment analysis: analyseDrugSetEnrichment(), loadDrugDescriptors(), plotDrugSetEnrichment()

Examples

descriptors <- loadDrugDescriptors("NCI60")
prepareDrugSets(descriptors)

nuno-agostinho/cTRAP documentation built on March 28, 2024, 3:59 p.m.