Description Usage Arguments Value See Also Examples
Filters the output of the EMVC algorithm to remove all annotations whose bootstrap annotation probability is below a specified threshold.
1 | filterAnnotations(annotations, proportion)
|
annotations |
Optimized annotation matrix returned by function |
proportion |
Threshold for annotation filtering. All annotations whose optimization proportion is below this value will be filtered. |
Updated version of the input annotation matrix that contains only those annotations with proportions greater than or equal to the specified threshold. Elements in this matrix are either 0 or 1.
EMVC
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1 2 3 4 5 6 7 8 9 10 11 12 | ## Create random optimized annotation matrix for 50 gene sets and 100 genes.
## This mimics what is generated by the EMVC() function
opt.annotations = matrix(runif(5000), nrow=50, ncol=100)
## Total number of non-zero annotations
length(which(opt.annotations > 0))
## Filter the results at .5 threshold. The number should be approximately half
## of the non-zero annotations since the proportions were generated as uniform(0,1)
filtered.opt.annotations = filterAnnotations(opt.annotations, .5)
sum(filtered.opt.annotations)
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