## barcodePattern ==============================================================
#' Single-sell barcode pattern
#'
#' Trailing number is to match cellranger output.
#'
#' @export
#' @note Updated 2023-09-21.
#'
#' @return `character(1)`.
#'
#' @examples
#' barcodePattern
barcodePattern <- ")_([ACGT_]{6,})(_[0-9]+)?$"
## genomeMetadataNames =========================================================
#' Slot names in metadata containing genome information
#'
#' @export
#' @note Updated 2023-09-21.
#'
#' @return `character`.
#'
#' @examples
#' genomeMetadataNames
genomeMetadataNames <- c("organism", "genomeBuild", "ensemblRelease")
## lanePattern =================================================================
#' Sequencing lane grep pattern
#'
#' @export
#' @note Updated 2023-09-21.
#'
#' @return `character(1)`.
#'
#' @examples
#' lanePattern
lanePattern <- "_L([[:digit:]]{3})"
## metadataDenylist ============================================================
#' Sample metadata denylist
#'
#' @export
#' @note Updated 2023-09-21.
#'
#' @details
#' `sampleId` (`sampleID` for older datasets) is set automatically for
#' multiplexed / cell-level data.
#'
#' @return `character`.
#'
#' @examples
#' metadataDenylist
metadataDenylist <- sort(c(
## Automatic / used internally:
## > "sampleID",
## > "sampleId",
"interestingGroups",
"revcomp",
"rowname",
## interestingGroups variants:
"interestinggroups",
"intgroup",
## sampleId, sampleName variants:
"ID",
"Id",
"id",
"name",
"names",
"sample",
"samples",
"sampleid",
"sampleNames",
"samplename",
"samplenames"
))
## metricsCols =================================================================
#' Quality control metric columns
#'
#' Column names returned by `calculateMetrics()`.
#'
#' @export
#' @note Updated 2023-09-21.
#'
#' @details
#' Previously: `"nGene"`, `"log10GenesPerUMI"`.
#'
#' @return `character`.
#'
#' @examples
#' metricsCols
metricsCols <- c(
"nCount",
"nFeature",
"nCoding",
"nMito",
"log10FeaturesPerCount",
"mitoRatio"
)
## updateMessage ===============================================================
#' Update message
#'
#' @export
#' @note Updated 2023-09-21.
#'
#' @return `character(1)`.
#'
#' @examples
#' message(updateMessage)
updateMessage <- "Run 'updateObject()' to update your object."
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