Data Preparation - Matrix Filtering

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.

Examples

if(exists("dfm")){
  allelefreq <- process_rcpp(dfm, min.depth, max.depth.quantile.prob, trunc, error)
}