R/data.R

In benstory/mitoClone2: Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

#' Mitochondrial exclusionlist
#'
#' List of variants that are likely not true somatic mutations and should thus be excluded
#' @format A list with four entries:
#' #' \itemize{
#'   \item \emph{three}: Regions of the mitochondrial genome that are within 1 nt of a 3-mer homopolymer (e.g. AAA)
#'   \item \emph{mutaseq}: Mutations in the mitochondrial genome that were reoccuring across patients (present in more than one individual in the MutaSeq dataset)
#'   \item \emph{masked}: Regions of the mitochondrial genome that are soft-masked in the UCSC or Ensembl annotations
#'   \item \emph{rnaEDIT}: Regions of the mitochondrial genome that are thought to be subject to RNA-editing according to the REDIportal V2.0
#' }
#' @name data
"exclusionlists"

#' Allele Count tables
#'
#'M: Mutant allele counts; N: Reference allele counts. P1: Patient 1; P2: Patient 2
#' @format a data frame of variable sites (columns) across single cells (rows)
#' @name data
NULL

#'@rdname data
"M_P1"

#'@rdname data
"N_P1"

#'@rdname data
"M_P2"

#'@rdname data
"N_P2"