R/imports.R

#' @importClassesFrom GenomicRanges GenomicRanges
#' @importClassesFrom IRanges IRanges Ranges
#' @importClassesFrom S4Vectors DataFrame
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#' @importFrom IRanges end start width
#' @importFrom Matrix readMM writeMM
#' @importFrom S4Vectors DataFrame Rle head mcols mcols<- metadata metadata<-
#'   na.omit tail
#' @importFrom SingleCellExperiment reducedDimNames reducedDim
#' @importFrom SummarizedExperiment assayNames assayNames<- assay colData
#'   colData<- rowData rowData<- rowRanges
#' @importFrom acidbase basenameSansExt bapply compress compressExtPattern
#'   decompress dots extPattern fileExt formalsList initDir matchArgsToDoCall
#'   pasteURL realpath standardizeCall
#' @importFrom cli cli_alert cli_alert_info cli_alert_success cli_alert_warning
#'   cli_text
#' @importFrom data.table fread fwrite
#' @importFrom goalie assert allAreAtomic allAreExisting allAreFiles
#'   allAreNonExisting allAreURLs allHaveAccess areDisjointSets areSameLength
#'   areSetEqual formalCompress hasColnames hasCols hasDimnames hasInternet
#'   hasLength hasNames hasNoDuplicates hasRownames hasRows hasValidNames
#'   hasValidDimnames isAFile isAURL isAny isCharacter isFlag isMatchingRegex
#'   isScalar isString isSubset validNames
#' @importFrom methods as is slotNames validObject .hasSlot
#' @importFrom rtracklayer import
#' @importFrom stringr str_extract str_match str_subset
#' @importFrom utils download.file packageVersion
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## This is needed to properly declare S4 `as()` coercion methods.
#' @importFrom methods coerce
#' @exportMethod coerce
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steinbaugh/brio documentation built on Jan. 31, 2020, 11:59 p.m.