Based on supplied matrix with total depth and sequencing coverage for each
nucleotide (A, C, G, and T) this function remove all but single nucelotide polymorphisms.
When supplied, this function will filter on coverage or allele frequency. Finally, the function
samples a single allele frequency per site to avoid data duplication.
Usage
process_rcpp(x, mindepth, maxprob, trunc, error)
Arguments
- x
Matrix with five columns: Depth, A, C, G, and T.
- mindepth
Minimum depth, default = 15.
- maxprob
Maximum depth quantile cut off, default = 0.9.
- trunc
List of two values representing the lower and upper bounds, $c_L$ and $c_U$.
- error
Sequencing error rate.
Value
Numeric Matrix with total coverage and coverage for a randomly sampled allele.