CELLector.unicizeSamples: Unicize patient samples' identifiers

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

Unicize patient samples' identifiers

Description

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

Usage

CELLector.unicizeSamples(ctumours,
                         keepReplicates = TRUE)

Arguments

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).

Value

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

Author(s)

Hanna Najgebauer and Francesco Iorio

References

[1] Iorio, F. et al. A Landscape of Pharmacogenomic Interactions in Cancer. Cell 166, 740–754 (2016).

See Also

CELLector.PrimTum.BEMs

Examples

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)))

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