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#Generated by codetoolsBioC version 0.0.16
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#Timestamp: Tue Feb 14 10:11:41 2012
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#Imports: AnnotationDbi, Biobase, BiocGenerics, biomaRt, GenomicRanges,
# graphics, grDevices, grid, IRanges, lattice, methods, RColorBrewer,
# rtracklayer, stats, utils
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importClassesFrom(biomaRt, Mart)
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importClassesFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString)
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importClassesFrom(GenomicRanges, GRanges)
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importClassesFrom(BSgenome, BSgenome)
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importClassesFrom(GenomicFeatures, "TranscriptDb")
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importClassesFrom(IRanges, IRanges, GroupedIRanges, NormalIRanges)
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importClassesFrom(methods, ANY, character, className, data.frame, environment,
integer, list, logical, matrix, missing, "NULL", ".NULL",
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numeric, ObjectsWithPackage, ordered, signature, namedList,
listOfMethods, ".environment", sourceEnvironment, envRefClass,
refObjectGenerator)
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importClassesFrom(rtracklayer, UCSCData)
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importMethodsFrom(AnnotationDbi, colnames, get, ls, mget, tail)
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importMethodsFrom(Biobase, rowMedians)
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importMethodsFrom(BiocGenerics, cbind, duplicated, eval, intersect, lapply,
mapply, order, paste, pmax, pmin, rbind, sapply, setdiff,
table, tapply, unique)
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importMethodsFrom(BSgenome, providerVersion)
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importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", exonsBy, transcriptsBy, transcripts)
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importMethodsFrom(GenomicRanges, "elementMetadata<-", genome, "genome<-",
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seqlengths, seqnames, seqlevels, seqinfo, strand, "strand<-", seqnameStyle)
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importMethodsFrom(IRanges, as.data.frame, as.list, as.matrix, as.vector,
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"colnames<-", coverage, diff, disjointBins, end, "end<-", range,
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findOverlaps, findRun, gsub, ifelse, "%in%", levels, match,
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mean, ncol, nlevels, nrow, queryHits, ranges, "ranges<-", reduce, rev,
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Rle, rownames, "rownames<-", runmean, runValue, "runValue<-",
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score, sort, split, start, "start<-", sub, subjectHits,
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substring, t, tolower, unlist, values, "values<-", which,
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which.max, width, "width<-", elementMetadata, endoapply,
elementLengths)
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importMethodsFrom(methods, coerce, initialize, show)
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importMethodsFrom(rtracklayer, chrom, close, getTable, "tableName<-",
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ucscTableQuery, trackNames, tableNames)
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importFrom(Biobase, listLen, rowMax, rowMin)
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importFrom(Biostrings, DNAStringSet, BStringSet, DNAString, BString, reverseComplement)
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importFrom(BiocGenerics, getObjectSlots)
importFrom(biomaRt, getBM, useMart)
importFrom(GenomicRanges, GRanges)
importFrom(graphics, par)
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importFrom(grDevices, boxplot.stats, col2rgb, colorRampPalette, extendrange,
hsv, rgb2hsv)
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importFrom(grid, convertHeight, convertWidth, convertX, convertY,
current.transform, current.viewport, current.vpTree, dataViewport,
downViewport, gpar, grid.circle, grid.lines, grid.newpage,
grid.polygon, grid.rect, grid.segments, grid.text, grid.yaxis,
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popViewport, pushViewport, stringHeight, stringWidth, unit,
upViewport, viewport)
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importFrom(IRanges, IRanges, subseq)
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importFrom(lattice, current.panel.limits, panel.abline, panel.grid, panel.lines,
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panel.points, panel.polygon, panel.segments, panel.xyplot, panel.text,
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trellis.par.get)
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importFrom(methods, "@<-", as, callNextMethod, getClass, getClassDef, is, new,
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"slot<-", slotNames)
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importFrom(RColorBrewer, brewer.pal)
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importFrom(rtracklayer, GenomicData, ucscGenomes, browserSession)
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importFrom(stats, loess.smooth)
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importFrom(biovizBase, getBioColor)
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importFrom(utils, assignInNamespace, browseURL, head, write.table)
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export(".chrName",
".doCache",
"AlignedReadTrack",
"AnnotationTrack",
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"DetailsAnnotationTrack",
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"BiomartGeneRegionTrack",
"DataTrack",
"DisplayPars",
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"drawGD",
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"GeneRegionTrack",
"GenomeAxisTrack",
"IdeogramTrack",
"UcscTrack",
"as.list",
"availableDisplayPars",
"clearSessionCache",
"exportTracks",
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"plotTracks",
"SequenceTrack")
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exportClasses("AlignedReadTrack",
"AnnotationTrack",
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"DetailsAnnotationTrack",
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"BiomartGeneRegionTrack",
"DataTrack",
"DisplayPars",
"GeneRegionTrack",
"GenomeAxisTrack",
"IdeogramTrack",
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"ImageMap",
"SequenceTrack")
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exportMethods("[",
"as.list",
"chromosome",
"chromosome<-",
"coerce",
"coords",
"coverage",
"displayPars",
"displayPars<-",
"elementMetadata<-",
"end",
"end<-",
"exon",
"exon<-",
"feature",
"feature<-",
"gene",
"gene<-",
"genome",
"genome<-",
"getPar",
"group",
"group<-",
"head",
"identifier",
"identifier<-",
"imageMap",
"initialize",
"length",
"max",
"min",
"names",
"names<-",
"position",
"range",
"ranges",
"score",
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"seqnames",
"seqlevels",
"seqinfo",
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"setPar",
"split",
"stacking",
"stacking<-",
"stacks",
"start",
"start<-",
"strand",
"strand<-",
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"subseq",
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"subset",
"symbol",
"symbol<-",
"tags",
"tail",
"transcript",
"transcript<-",
"values",
"values<-",
"width",
"width<-")
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