R/imports.R

## S4 classes ==================================================================

#' @importClassesFrom AcidBase missingOrNULL
#' @importClassesFrom AcidGenomes Tx2Gene
#' @importClassesFrom DESeq2 DESeqDataSet DESeqTransform
#' @importClassesFrom IRanges DataFrameList
#' @importClassesFrom SummarizedExperiment RangedSummarizedExperiment
#' SummarizedExperiment
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## S4 generics and methods =====================================================

#' @importFrom AcidGenerics Gene2Symbol alphaSummary alphaThreshold
#' alphaThreshold<- as.DESeqDataSet as.DESeqTransform autopadZeros
#' baseMeanThreshold baseMeanThreshold<- camelCase contrastName contrastName<-
#' contrastSamples convertGenesToSymbols convertSampleIDsToNames correlation
#' deg degIntersection degPerContrast droplevels2 interestingGroups
#' interestingGroups<- intersectionMatrix leftJoin lfcShrink lfcShrink<-
#' lfcShrinkType lfcThreshold lfcThreshold<- makeNames mapGenesToSymbols
#' markdownTables melt metadata2 metadata2<- plotBaseMean plotContrastScatter
#' plotCorrelationHeatmap plotCounts plotDEGHeatmap plotDEGPCA plotDEGStackedBar
#' plotDEGUpset plotHeatmap plotLFC plotQuantileHeatmap plotUpset plotVolcano
#' removeNA results resultsDiff resultsMatrix resultsNames resultsNames<-
#' resultsTables sampleData snakeCase transformType
#' @importFrom BiocGenerics Map anyDuplicated as.data.frame cbind combine counts
#' design do.call plotPCA plotMA unlist updateObject
#' @importFrom DESeq2 priorInfo
#' @importFrom S4Vectors complete.cases cor decode droplevels head mcols mcols<-
#' metadata metadata<- na.omit
#' @importFrom SummarizedExperiment assays assays<- colData colData<- rowData
#' @importFrom methods coerce show
#' @importFrom pipette export import
#'
#' @importMethodsFrom AcidBase intersectionMatrix
#' @importMethodsFrom AcidExperiment Gene2Symbol autopadZeros
#' convertGenesToSymbols convertSampleIDsToNames droplevels2 export
#' interestingGroups interestingGroups<- mapGenesToSymbols melt
#' @importMethodsFrom AcidGenomes Gene2Symbol
#' @importMethodsFrom AcidPlots plotCounts plotHeatmap plotPCA plotUpset
#' @importMethodsFrom AcidPlyr leftJoin melt
#' @importMethodsFrom DESeq2 counts design
#' @importMethodsFrom pipette droplevels2 export import metadata2 metadata2<-
#' removeNA
#' @importMethodsFrom syntactic autopadZeros camelCase makeNames snakeCase
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## S3 generics =================================================================

#' @importFrom stats model.matrix relevel
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## Standard functions ==========================================================

#' @importFrom AcidBase initDir methodFunction printString realpath
#' requireNamespaces showSlotInfo standardizeCall
#' @importFrom AcidCLI abort alert alertInfo alertWarning dl toInlineString
#' @importFrom AcidMarkdown markdownHeader markdownList
#' @importFrom AcidPlots !! acid_coord_flip acid_geom_label_repel
#' autoDiscreteColorScale autoDiscreteFillScale matchLabels pretty_breaks sym
#' wrap_plots
#' @importFrom DESeq2 DESeq fpkm nbinomWaldTest
#' @importFrom IRanges DataFrameList
#' @importFrom S4Vectors DataFrame SimpleList
#' @importFrom ggplot2 aes after_stat annotation_logticks element_blank geom_bar
#' geom_density geom_freqpoly geom_hline geom_point geom_text geom_vline ggplot
#' guides labs position_stack scale_color_manual scale_x_continuous
#' scale_y_continuous theme
#' @importFrom goalie allArePositive areDisjointSets areIntersectingSets
#' areSameLength areSetEqual assert bapply hasColnames hasLength hasNames
#' hasLength hasRows hasRownames hasValidDimnames hasValidNames isAFile
#' isAlpha isAny isCharacter isFlag isHeaderLevel isInRange isInt
#' isMatchingFixed isNegative isNonNegative isNumber isPercentage isPositive
#' isScalar isString isSubset validate
#' @importFrom methods as is new prototype setClass setGeneric setValidity slot
#' slot<- validObject .hasSlot
#' @importFrom stringi stri_match_first_regex
#' @importFrom utils capture.output getS3method packageName packageVersion
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steinbaugh/DESeqAnalysis documentation built on Sept. 5, 2022, 3:55 p.m.