R/sampleMetagenomeResults.R

In ProActive: Detect Elevations and Gaps in Mapped Sequencing Read Coverage

#' sampleMetagenomeResults
#'
#' Output of `ProActiveDetect()`
#' Report...
#'
#' @keywords internal
#' @format ## `sampleMetagenomeResults`
#' A list with 6 objects:
#' \describe{
#'   \item{SummaryTable}{A table containing all pattern-matching classifications}
#'   \item{CleanSummaryTable}{A table containing only gap and elevation pattern-match
#' classifications (i.e. noPattern classifications removed)}
#'   \item{PatternMatches}{A list object containing information needed to visualize the
#' pattern-matches in `plotProActiveResults()`}
#'   \item{FilteredOut}{A table containing contigs/chunks that were filtered out for being
#' too small or having too low read coverage}
#'   \item{Arguments}{A list object containing arguments used for pattern-matching (windowSize,
#' mode, chunkSize, chunkContigs)}
#'   \item{GeneAnnotTable}{A table containing gene predictions associated with elevated
#' or gapped regions in pattern-matches}
#' }
#' @details This data was generated by running `ProActiveDetect()` on the sampleMetagenomePileup
#' and sampleMetagenomegffTSV with default parameters.
"sampleMetagenomeResults"