PharmacoGx (version 1.1.6)

intersectPSet: 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)

Arguments

pSets

[list] a list of PharmacoSet objects, of which the function should find the intersection

intersectOn

[character] which identifiers to intersect on, drugs or cell lines

cells

a vector 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 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?

Value

[list] 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