R/data.R

In scruff: Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

#' A vector of example cell barcodes.
#'
#' A vector containing 48  predefined cell barcodes which
#'  will be used for
#'  demultiplexing the example FASTQ files. Only the cell barcodes from 49 to
#'  96 of the original 96 barcodes are used here to reduce the time to run
#'  example codes and compile the vignette.
#'
#' @format A vector of cell barcode sequences. Cell barcodes for this study
#'  (van den Brink, et al.) are of length 8.
"barcodeExample"

#' Example SingleCellExperiment Object
#'
#' An example SingleCellExperiment object containing count matrix, cell and
#'  gene annotations, and all QC metrics for mouse mitochonrial genes generated
#'  from example FASTQ reads.
#'
#' @format A \code{SingleCellExperiment} object.
"sceExample"

#' Example GAlignments Object
#'
#' An example GAlignments object containing read alignment information for cell
#'  "vandenBrink_b1_cell_0095" of example FASTQ files. Used as an example for
#'  \code{rview} function.
#'
#' @format A \code{GAlignments} object.
"bamExample"

#' Cell barcode whitelist (737K-august-2016.txt)
#'
#' A barcode whitelist is the list of all known barcode sequences that have
#'  been included in the assay kit and are available during library preparation.
#'  There are roughly 737,000 cell barcodes in the whitelist
#'  (737K-august-2016.txt) for Cell Ranger's
#'  Single Cell 3' and V(D)J applications.
#'
#' @format A \code{data.table} object.
"validCb"

#' Top 10,000 rows for v1, v2, and v3 cell barcode whitelist files
#'
#' The first 10,000 cell barcodes in v1 (737K-april-2014_rc.txt), v2
#'  (737K-august-2016.txt), and v3 (3M-february-2018.txt) cell barcode
#'  whitelist files. This object is used for testing the validity of input
#'  assay chemistry \code{validCb} for \link{tenxBamqc} function. The cell
#'  barcodes for the first 10,000 alignments in the input BAM file will be
#'  mapped to each chemistry's whitelist to determine the assay chemistry of
#'  the BAM file.
#'
#' @format A \code{data.table} object.
"cbtop10000"