x is a matrix of 0's and 1's. Each column represents a sample (cell-line, individual, etc.) while each column represents an amino acid in the protein. The i-th column represents the i-th amino acid.
alpha
The significance level to be used.
multtest
The type of multiple comparisons adjustment to be used.
Value
Returns a matrix of results which include the starting and ending positions of the clusters along with a p-value for each cluster.
References
Ye et. al., Statistical method on nonrandom clustering with application to somatic mutations in cancer. BMC Bioinformatics. 2010. doi:10.1186/1471-2105-11-11.