CELLector.visualiseSearchingSpace | R Documentation |
This function visualise the CELLector searching space as an interactive collapsible tree. Moving the mouse over the nodes of this tree shows patients' subtype details and (optionally) matched cell lines
CELLector.visualiseSearchingSpace(searchSpace, CLdata = NULL)
searchSpace |
A CELLector searching space as returned by the
|
CLdata |
If different from |
Hanna Najgebauer and Francesco Iorio
[1] Forbes, S. A. et al. COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805–11 (2015).
[2] Iorio, F. et al. A Landscape of Pharmacogenomic Interactions in Cancer. Cell 166, 740–754 (2016).
CELLector.Build_Search_Space
,
CELLector.CellLine.BEMs
data(CELLector.PrimTum.BEMs)
data(CELLector.Pathway_CFEs)
data(CELLector.CFEs.CNAid_mapping)
data(CELLector.CFEs.CNAid_decode)
data(CELLector.HCCancerDrivers)
data(CELLector.CellLine.BEMs)
tumours_BEM<-CELLector.PrimTum.BEMs$COREAD
CELLlineData<-CELLector.CellLine.BEMs$COREAD
### unicize the sample identifiers for the tumour data
tumours_BEM<-CELLector.unicizeSamples(tumours_BEM)
### building the CELLector searching space
CSS<-CELLector.Build_Search_Space(ctumours = t(tumours_BEM),
verbose = FALSE,
minGlobSupp = 0.05,
cancerType = 'COREAD',
pathway_CFEs = CELLector.Pathway_CFEs,
cnaIdMap = CELLector.CFEs.CNAid_mapping,
mutOnly = FALSE,
cnaIdDecode = CELLector.CFEs.CNAid_decode,
cdg = CELLector.HCCancerDrivers)
### visualising the Searching space as collapsible tree
CELLector.visualiseSearchingSpace(searchSpace = CSS,CLdata = CELLlineData)
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