removeLowFreqs: Removes alterations based on frequency
In cbg-ethz/TiMEx: Finding Mutually Exclusive Groups of Alterations in Cancer Datasets

Description Usage Arguments Details Value Author(s) References See Also Examples

removeLowFreqs returns a binary matrix from which genes altered with lower frequency than the input level are removed.

1	removeLowFreqs(mat, level)

`mat`	binary alteration matrix, with rows representing patients and columns representing genes
`level`	frequency level under which the genes are to be removed (real number between 0 and 1). Default is 0.03.

It is only recommended to run this function if the user is not at all interested in the role of low-frequently altered genes.

the binary input matrix without the low-frequently altered genes.

Simona Cristea, scristea@jimmy.harvard.edu

Constantinescu et al.: TiMEx: A Waiting Time Model for Mutually Exclusive Cancer Alterations. Bioinformatics (2015).

ovarian, breast, and gbmDendrix for examples of biological large cancer datasets.

# Remove genes altered in less than 3% (the default level) of the samples  
# in the ovarian cancer dataset
data(ovarian)
ovarianNew<-removeLowFreqs(ovarian)