import(methods) importFrom(utils, read.delim, .DollarNames) importFrom(stats, setNames) importClassFrom(Matrix, Matrix) # for the "acbind" and "arbind" methods import(BiocGenerics) import(S4Vectors) import(IRanges) import(GenomeInfoDb) import(GenomicRanges) import(Biobase) ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### Export S4 classes ### exportClasses( Assays, ShallowData, ShallowSimpleListAssays, SummarizedExperiment, SummarizedExperiment0, RangedSummarizedExperiment ) ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### Export S4 methods for generics not defined in SummarizedExperiment ### exportMethods( length, names, "names<-", dim, dimnames, "dimnames<-", "[", "[<-", "[[", "[[<-", "$", "$<-", as.data.frame, coerce, show, c, merge, Compare, ## Generics defined in BiocGenerics: cbind, rbind, duplicated, match, is.unsorted, order, rank, sort, start, "start<-", end, "end<-", width, "width<-", strand, "strand<-", updateObject, ## Generics defined in S4Vectors: "metadata<-", mcols, "mcols<-", elementMetadata, "elementMetadata<-", values, "values<-", extractROWS, replaceROWS, subset, pcompare, ## Generics defined in IRanges: ranges, "ranges<-", shift, narrow, resize, flank, promoters, restrict, trim, isDisjoint, disjointBins, coverage, findOverlaps, precede, follow, nearest, distance, distanceToNearest, acbind, arbind, ## Generics defined in GenomeInfoDb: seqinfo, "seqinfo<-", seqnames, "seqnames<-" ) ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### Export non-generic functions ### export( Assays, .DollarNames.SummarizedExperiment, makeSummarizedExperimentFromExpressionSet, makeSummarizedExperimentFromDataFrame, naiveRangeMapper, probeRangeMapper, geneRangeMapper, readKallisto, readKallistoBootstrap, KALLISTO_ASSAYS ) ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### Export S4 generics defined in SummarizedExperiment + export corresponding ### methods ### export( SummarizedExperiment, rowRanges, "rowRanges<-", rowData, "rowData<-", colData, "colData<-", assayNames, "assayNames<-", assays, "assays<-", assay, "assay<-" ) ### Exactly the same list as above. exportMethods( SummarizedExperiment, rowRanges, "rowRanges<-", rowData, "rowData<-", colData, "colData<-", assayNames, "assayNames<-", assays, "assays<-", assay, "assay<-" ) ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ### Register S3 methods ### S3method(.DollarNames, SummarizedExperiment)