CELLector.visualiseSearchingSpace: Visualising the CELLector searching space as a collapsibe...

In najha/CELLector: Genomics guided selection of cancer cell lines

Visualising the CELLector searching space as a collapsibe tree

Description

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

Usage

CELLector.visualiseSearchingSpace(searchSpace, CLdata = NULL)

Arguments

searchSpace

A CELLector searching space as returned by the CELLector.Build_Search_Space function

CLdata

If different from NULL (default) this argument must contain a data frame in which the first two columns contain the COSMIC [1] identiefiers and names of cell lines (one per row), respectively, and then binary entries indicating the status of cancer functional events (CFEs, as defined in [2], one per column) across cell lines. The format is the same of the entries of the list in the built-in CELLector.CellLine.BEMs. Based on this data the cell lines are mapped onto the CELLector searching space and the number of cell lines mapped in each subtype showed when moving the mouse on the corresponding node.

Author(s)

Hanna Najgebauer and Francesco Iorio

References

[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).

See Also

CELLector.Build_Search_Space,

CELLector.CellLine.BEMs

Examples

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)

najha/CELLector documentation built on Feb. 8, 2023, 5:35 a.m.