R/baf_summary.R

In knausb/coveRage: Tools to Explore Sequencing Coverage in High-Throughput Sequencing Projects

#' @title Summarize baf count tables
#' @name baf_summary
#' @rdname baf_summary
#' 
#' @description Calculate summary statistics for count tables produced by baf_stats
#' 
#' @param counts count table produced by baf_stats
#' @param probs vector of probabilities to pass to quantile
#' 
#' @details
#' This function is intended to summarize count tables produced by baf_stats.
#' By default the mean, variance and five quantiles (0.025, 0.16, 0.5, 0.84, 0.975) are returned.
#' The quantiles are generated by the function quantile and may be changed by changing the option probs.
#' 
#' @return a vector of size two plus the number of quantiles requested.
#' 
#' 
#' @seealso baf_stats, quantile
#' 
#' @export
baf_summary <- function(counts, probs=c(0.025, 0.16, 0.5, 0.84, 0.975)){
  x <- vector(mode="numeric", length=length(probs)+2)
  x[1] <- mean(rowSums(counts[,-1]))
  x[2] <- stats:: var(rowSums(counts[,-1]))
  names(x)[1:2] <- c("mean", "variance")
  quants <- stats::quantile(rowSums(counts[,-1]), probs=probs)
  x[-c(1,2)] <- quants
  names(x)[-c(1,2)] <- names(quants)
  x
}