CELLector.unicizeSamples | R Documentation |
This function checks if there are multiple samples derived from the same patients in the binary event matrix (BEM) modeling the presence/absence of the cancer functional events (CFEs, defined in [1]), in the cancer patients. These can be mantained (and in this case their identifier will be made unique) or discarded
CELLector.unicizeSamples(ctumours,
keepReplicates = TRUE)
ctumours |
A binary matrix with entries indicating the status (Present/Absent) of each CFE (one per row) across primary tumors samples (one per column). |
keepReplicates |
A boolean value indicating whether the duplicated samples should be kept (and their identifier made unique, by adding a progressive numerical suffix) or discarded (in this case only one sample per patient will be kept and identifiers unchanged). |
A binary matrix with entries indicating the status (Present/Absent) of each CFE (one per row) across primary tumors samples (one per column), and with unique patients' (column) identifiers
Hanna Najgebauer and Francesco Iorio
[1] Iorio, F. et al. A Landscape of Pharmacogenomic Interactions in Cancer. Cell 166, 740–754 (2016).
CELLector.PrimTum.BEMs
data(CELLector.PrimTum.BEMs)
tumours_data<-CELLector.PrimTum.BEMs$COREAD
dim(tumours_data)
length(unique(colnames(tumours_data)))
tumours_data<-CELLector.unicizeSamples(tumours_data)
dim(tumours_data)
length(unique(colnames(tumours_data)))
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