DEUS: Differential expression of unique sequences

#*  Copyright (C) 2018 the DEUS contributors.
#*  Website: https://github.com/timjeske/DEUS
#*
#*  This file is part of the DEUS R package.
#*
#*  The DEUS R package is free software: you can redistribute it and/or modify
#*  it under the terms of the GNU General Public License as published by
#*  the Free Software Foundation, either version 3 of the License, or
#*  (at your option) any later version.
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#*  This program is distributed in the hope that it will be useful,
#*  but WITHOUT ANY WARRANTY; without even the implied warranty of
#*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#*  GNU General Public License for more details.
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#' Compute fraction of reads without BLAST hit for each sample
#'
#' @param summary Summary table generated by \link[DEUS]{mergeResults} (requires BLAST result generated by \link[DEUS]{runBlast})
#' @param count_table A table of (normalized) sequence counts.
#' A sequence count table can be generated by \link[DEUS]{createCountTableFromFastQs} and normalized by applying \link[DEUS]{runDESeq2}
#' @return A data frame with samples as row names and the column 'NA_fraction'
#' @export

getNoBlastHitFraction <- function(summary, count_table) {

  if(!("FeatureList" %in% names(summary))) stop('Feature classes can only be counted if blast results have been merged to DE results!')

  minql <- min(summary[summary$FeatureList!="NA",]$Length, na.rm=T)
  summary <- summary[summary$Length >= minql,]

  select <- row.names(summary)[summary$FeatureList=="NA"]
  sub <- count_table[as.vector(select),,drop = FALSE]
  res <- colSums(sub)/colSums(count_table)
  res <- as.data.frame(res)
  colnames(res) <- c("NA_fraction")
  return(res)
}