R/sampleMetagenomePileup.R

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

#' sampleMetagenomePileup
#'
#' A subset of contigs from the raw whole-community fraction read coverage
#' pileup file generated during read mapping.
#' Report...
#'
#' @keywords internal
#' @format ## `sampleMetagenomePileup`
#' A data frame with 4,604 rows and 4 columns:
#' \describe{
#'   \item{V1}{Contig accession}
#'   \item{V2}{Mapped read coverage averaged over a 100 bp window size}
#'   \item{V3}{Starting position (bp) of each 100 bp window. Restarts from 0 at
#'  the start of each new contig.}
#'   \item{V4}{Starting position (bp) of each 100 bp window. Does NOT restart at
#'  the start of each new contig.}
#' }
#' @details This dataset was generated from a conventional mouse fecal
#' homogenate. The whole-community extracted DNA was sequenced with Illumina
#' (paired-end mode, 150 bp reads) after which the metagenome was assembled. The
#' sequencing reads were mapped to the assembled contigs using BBMap. The
#' bbmap.sh bincov parameter with covbinsize=100 was used to create a pileup
#' file with 100 bp windows. A subset of 10 contigs from the pileup file were
#' selected for this sample dataset. The contigs were chosen because their
#' associated read coverage patterns exemplify ProActive's
#' pattern-matching and characterization functionality across classifications:
#' NODE_1911: elevation off left
#' NODE_1583: elevation off right
#' NODE_1884: gap off right
#' NODE_1255: gap off left
#' NODE_368: full gap
#' NODE_617: elevation full
#' NODE_1625: no pattern
#' @source
#' <https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00935-5>
"sampleMetagenomePileup"