panDrugGraph: Drug Network Graph

In sinnweja/panoply: Personalized Cancer Report

Description

Graph that shows the connection between the drugs, genes and pathways for the drugs that target the most genes

Usage

panDrugGraph(panDrug,usePathIDs = TRUE, ndrugs=8)

Arguments

panDrug	A data.frame of drug test results from panDrugSets
usePathIDs	If TRUE the shorter reactome pathway IDs will be used in the graph instead fo the complete name
ndrugs	Minimum number of Drugs to include in the graph

Details

Graph where Drugs=Red Ellipse, Genes=Blue Ellipse, Pathways=Green Rectangles

Value

Nothing is returned

Examples

data(clinPanTNBC)
data(genelistPan)
data(cnaPanTNBC)
data(gcPanTNBC)
data(gcinfoPan)
data(variantPanTNBC)
data(dgidbPan)
data(dgiSets)
data(reactome)
patient <- "TCGA-B6-A0IK"
match.index <- which(clinPanTNBC$Vital.Status=="Alive" & clinPanTNBC$PatientID!=patient & clinPanTNBC$age_at_diagnosis>50 & clinPanTNBC$N.stage == "N1" & clinPanTNBC$ndays > 1000)
ptmatch <- clinPanTNBC[match.index,"PatientID"]
drivGenes <- panGeneSets(caseid=patient, controlid=ptmatch, eventOnly=TRUE, variant=variantPanTNBC,
  cna=cnaPanTNBC, gcount=gcPanTNBC, tumorpct=0.3, tailEnd="upper", tailPct=0.1)
set.seed(1000)
drugResults <- panDrugSets(drivGenes, caseids=patient,
  controlids=ptmatch, gcount=gcPanTNBC,nsim=200, tailEnd="upper") 
drugResults<- drugResults[!is.na(drugResults$Pathways) & !is.na(drugResults$N.Cancer.Genes),]
panDrugGraph(drugResults)

sinnweja/panoply documentation built on Aug. 9, 2019, 9:56 a.m.