CELLector.mostSupported_CFEs | R Documentation |
This function identifies the most frequent combination of cancer functional events (CFEs) in a large cohort of cancer patients.
CELLector.mostSupported_CFEs(transactions,
minSupport = 0.05,
minlen = 1,
maxLen = 10)
transactions |
A named binary matrix with CFEs on the rows, samples on the columns and entries specifying the presence/absence of a given CFE in a given sample: the transactions object. |
minSupport |
The minimal support that a combination of CFEs must have, i.e. the minimal ratio of samples in which the CFEs must be observed simoultanously, in order to be considered in the analysis. |
minlen |
The minimal length of a combination of CFEs (of how many indivudal CFE it needs to be composed) in order to be considered in the analysis (1 by default). |
maxLen |
The maximal length of a combination of CFEs (the maximal number of indivudal CFEs) in order to be considered in the analysis (10 by default). |
This function uses the eclat function from the R package arules.
A list with the following fields:
MSIS |
A string or a vector of strings (depending on the argument |
SUPPORT |
The ratio of samples where the combination of CFEs in |
absSUPPORT |
The number of samples where the combination of CFEs in |
supportingSamples |
The identifiers of the samples supporting |
Hanna Najgebauer and Francesco Iorio
Najgebauer et al., CELLector: Genomics Guided Selection of Cancer in vitro Models.
doi:10.1101/275032
data(CELLector.PrimTum.BEMs)
RES<-CELLector.mostSupported_CFEs(transactions = t(CELLector.PrimTum.BEMs$COREAD),
minlen = 2)
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