intersectPSet {PharmacoGx} | R Documentation |
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
intersectPSet(pSets, intersectOn = c("drugs", "cell.lines", "concentrations"), cells, drugs, strictIntersect = FALSE, verbose = TRUE, nthread = 1)
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 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? |
nthread |
[numeric] The number of cores to use to run intersection on concentrations |
[list] a list of pSets, contatining only the intersection
data(GDSCsmall) data(CCLEsmall) common <- intersectPSet(list('GDSC'=GDSCsmall, 'CCLE'=CCLEsmall), intersectOn = c("drugs", "cell.lines")) common$CGP common$CCLE