R/sampleGenomePileup.R

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

#' sampleGenomePileup
#'
#' A pileup file generated during read mapping to the *Salmonella enterica* LT2 genome.
#' Report...
#'
#' @keywords internal
#' @format ## `sampleGenomePileup`
#' A data frame with 48,575 rows and 4 columns:
#' \describe{
#'   \item{V1}{Accession}
#'   \item{V2}{Mapped read coverage averaged over a 100 bp window size}
#'   \item{V3}{Starting position (bp) of each 100 bp window. Starts from 100.}
#'   \item{V4}{Starting position (bp) of each 100 bp window. Starts from 0.}
#' }
#' @details This dataset was generated by extracting DNA from a culture of
#' *Salmonella enterica* LT2 (LT2) infected with phage P22. The DNA was shotgun
#' sequenced with Illumina (paired-end mode, 150 bp reads). The sequencing reads
#' were mapped to the LT2 reference genome (NCBI RefSeq NC_003197.2). The
#' bbmap.sh bincov parameter with covbinsize=100 was used to create a pileup file
#' with 100 bp windows.
#' @source
#' <https://pubmed.ncbi.nlm.nih.gov/25608871/>
"sampleGenomePileup"