intersectPSet: Intersects objects of the PharmacoSet class, subsetting them...

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

Intersects objects of the PharmacoSet class, subsetting them to the common drugs and/or cell lines as selected by the user.

Description

Given a list of PharmacoSets, the function will find the common drugs, and/or cell lines, and return PharmacoSets that contain data only pertaining to the common drugs, and/or cell lines. The mapping between dataset drug and cell names is done using annotations found in the PharmacoSet object's internal curation slot

Usage

intersectPSet(
  pSets,
  intersectOn = c("drugs", "cell.lines", "concentrations"),
  cells,
  drugs,
  strictIntersect = FALSE,
  verbose = TRUE,
  nthread = 1
)

Arguments

pSets	list a list of PharmacoSet objects, of which the function should find the intersection
intersectOn	character which identifiers to intersect on, drugs, cell lines, or concentrations
cells	a charactervector of common cell lines between pSets. In case user is intersted on getting intersection on certain cell lines, they can provide their list of cell lines
drugs	a character vector of common drugs between pSets. In case user is intersted on getting intersection on certain drugs, they can provide their list of drugs.
strictIntersect	boolean Should the intersection keep only the drugs and cell lines that have been tested on together?
verbose	boolean Should the function announce its key steps?
nthread	numeric The number of cores to use to run intersection on concentrations

Value

A list of pSets, contatining only the intersection

Examples

data(GDSCsmall)
data(CCLEsmall)
common <- intersectPSet(list('GDSC'=GDSCsmall,'CCLE'=CCLEsmall),
                        intersectOn = c("drugs", "cell.lines"))
common$CGP
common$CCLE

bhklab/PharmacoGx documentation built on April 18, 2024, 3:13 a.m.