CELLector.selectionVisit: Visiting the CELLector searching space

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

Visiting the CELLector searching space

Description

This function visits the CELLector searching space using the greedy algorithm described in [1] and it returns the cancer patients subtypes identifiers sorted for cell line selection, maximising the genomic heterogeneity observed in the analysed cohort of cancer patients when considering the first n subtypes.

Usage

CELLector.selectionVisit(TAV)

Arguments

TAV	A CELLector searching space stored as a Navigable Table, outputted by the CELLector.Build_Search_Space function

Value

A numerical vector containing the subtypes identifers sorted as explained above

Author(s)

Hanna Najgebauer and Francesco Iorio

References

[1] Najgebauer, H. et al. Genomics Guided Selection of Cancer in vitro Models.

https://doi.org/10.1101/275032

See Also

CELLector.Build_Search_Space

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)

CELLector.selectionVisit(CSS$navTable)

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