nmc {iPAC} | R Documentation |
This runs the clustering algorithm developed by Ye. et. al on the original linear protein.
nmc(x, alpha = 0.05, multtest = c("Bonferroni", "BH", "None"))
x |
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. |
Returns a matrix of results which include the starting and ending positions of the clusters along with a p-value for each cluster.
Please see the original paper and methodology for a more detailed description of each of the parameters to this function.
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.
data(KRAS.Mutations) nmc(KRAS.Mutations, alpha = 0.05, multtest = "Bonferroni")