R/tetramers-package.R

In BigelowLab/tetramers: Tetramer Analysis with Principle Component Analysis

#' tetramers
#'
#' tetramers detects outlier regions in genomes in terms of tetramer composition,
#' which are indicative of either contamination or gene transfer. Tetramers along
#' a contig are tabulated by sliding a window along the length each contig.
#'
#' @name tetramers-package
#' @docType package
#' @importFrom dplyr %>%
#' @importFrom rlang .data
#' @importFrom R6 R6Class
NULL

#' A gobal variable to store defaults for the tetramerPCA.
#'
#' @format A list of global constants and defaults
#' \describe{
#'    \item{WINDOW}{the window of analysis in bases - this windows 'slides' along the contig}
#'    \item{STEP}{the distance in bases to advance the window between successive tabulations}
#'    \item{WIDTH}{here it is always 4 bases per polymer, but the idea is that eventually other widths maybe possible}
#'    \item{NAME}{currently unused}
#'    \item{NPC}{The number of principle components to retain, by default 8}
#'    \item{CLEAN}{logical, if TRUE then attempt to clean the inut contigs of disallowed characters}
#'    \item{VERBOSE}{logical, if TRUE then output informational messages}
#'    \item{LOG}{the name of the output log file, if used}
#'    \item{PICK}{the number of outliers to select per PC, by default 2}
#'    \item{PAIRS}{a two column matrix specifing the PCs to juxtapose}
#'    \item{BLASTPATH}{the path to the location of the local install of blastn}
#'    \item{DNALETTERS}{a list of allowed DNA letters}
#'    \item{TETRAMERS}{a list of reverse-complimented tabulated tetramers, length = 136}
#'    \item{UTETRAMERS}{a list of possible tetramers, some of which may be reverse compliments, length = 256}
#'    \item{FAILSTATUS}{a list of reasons why a contig may fail the tetramerPCA process }
#'    \item{BLASTOPTS}{a list of default blastn options}
#' }
"TETRA"