betabinLRT {deepSNV} | R Documentation |
Maximum likelihood version of Shearwater producing p-values instead of Bayes factors.
betabinLRT(counts, rho = NULL, truncate = 0.05, rho.min = 1e-04, rho.max = 0.8, maxvaf = 0.3, mindepth = 10, maxtruncate = 0.5)
counts |
The array of counts typically generated by loadAllData. |
rho |
Use this variable to fix the dispersion parameter to a value of interest. Default: NULL, rho will be estimated from the data. |
truncate |
Samples with variant allele frequencies higher than "truncate" will be excluded from the background error model. |
rho.min |
If rho=NULL, rho will be estimated from the data in the interval [rho.min,rho.max]. |
rho.max |
If rho=NULL, rho will be estimated from the data in the interval [rho.min,rho.max]. |
maxvaf |
Sites with an average rate of mimatches higher than maxvaf will not be considered (e.g. SNPs or reference sites). |
mindepth |
Minimum coverage required to test a site. |
maxtruncate |
Maximum number of samples that can be excluded from the background error model by truncate for a site to be tested. |
A list with two arrays for P- and Q-values.
Inigo Martincorena and Moritz Gerstung
Martincorena I, Roshan A, Gerstung M, et al. (2015). High burden and pervasive positive selection of somatic mutations in normal human skin. _Science_ (Under consideration).
# code to be added