409 lines
9.6 KiB
Plaintext
409 lines
9.6 KiB
Plaintext
useDynLib(IRanges)
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import(methods)
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importFrom(utils, stack, read.table)
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importFrom(stats, cov, cor, median, quantile,
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smoothEnds, runmed, "window<-", aggregate,
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setNames)
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import(BiocGenerics)
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import(S4Vectors)
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importFrom(stats4, summary)
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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### Export S4 classes
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###
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exportClasses(
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## DataFrameList-class.R:
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DataFrameList, DFrameList,
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SimpleDataFrameList, SimpleDFrameList,
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SplitDataFrameList, SplitDFrameList,
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SimpleSplitDataFrameList, SimpleSplitDFrameList,
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## AtomicList-class.R:
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AtomicList, SimpleAtomicList,
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LogicalList, SimpleLogicalList,
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IntegerList, SimpleIntegerList,
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NumericList, SimpleNumericList,
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ComplexList, SimpleComplexList,
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CharacterList, SimpleCharacterList,
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RawList, SimpleRawList,
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RleList, SimpleRleList,
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FactorList, SimpleFactorList,
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## Ranges-and-RangesList-classes.R:
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Ranges, IntegerRanges, Pos,
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RangesList, SimpleRangesList,
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IntegerRangesList, SimpleIntegerRangesList,
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PosList, SimplePosList,
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## IPosRanges-class.R:
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IPosRanges,
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## IntegerRangesList-class.R
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IntegerRangesList, SimpleIntegerRangesList,
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## IRanges-class.R:
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IRanges, NormalIRanges,
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## IPos-class.R:
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IPos, UnstitchedIPos, StitchedIPos,
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## Grouping-class.R:
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Grouping, ManyToOneGrouping, ManyToManyGrouping,
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H2LGrouping, Dups,
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GroupingRanges, GroupingIRanges,
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Partitioning, PartitioningByEnd, PartitioningByWidth, PartitioningMap,
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## Views-class.R:
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Views,
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## RleViews-class.R:
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RleViews,
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## SimpleGrouping-class.R:
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SimpleGrouping,
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SimpleManyToOneGrouping,
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BaseManyToManyGrouping,
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SimpleManyToManyGrouping,
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## IRangesList-class.R:
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IRangesList, SimpleIRangesList,
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NormalIRangesList, SimpleNormalIRangesList,
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## IPosList-class.R:
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IPosList, SimpleIPosList,
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## ViewsList-class.R:
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ViewsList, SimpleViewsList,
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## RleViewsList-class.R:
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RleViewsList, SimpleRleViewsList,
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## RangedSelection-class.R:
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RangedSelection,
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## MaskCollection-class.R:
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MaskCollection,
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## CompressedList-class.R:
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CompressedList,
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## CompressedDataFrameList-class.R:
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CompressedDataFrameList, CompressedDFrameList,
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CompressedSplitDataFrameList, CompressedSplitDFrameList,
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## CompressedAtomicList-class.R:
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CompressedAtomicList,
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CompressedLogicalList,
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CompressedIntegerList,
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CompressedNumericList,
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CompressedComplexList,
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CompressedCharacterList,
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CompressedRawList,
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CompressedRleList,
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CompressedFactorList,
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## CompressedGrouping-class.R:
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CompressedGrouping,
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CompressedManyToOneGrouping, CompressedManyToManyGrouping,
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## CompressedRangesList-class.R:
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CompressedRangesList, CompressedPosList,
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CompressedIntegerRangesList,
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CompressedIRangesList, CompressedNormalIRangesList, CompressedIPosList,
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## NCList-class.R:
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NCList, NCLists,
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## nearest-methods.R:
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IntegerRanges_OR_missing
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)
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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### Export S3 methods
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###
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S3method(as.data.frame, IPosRanges)
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S3method(as.data.frame, IPos)
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S3method(diff, AtomicList)
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S3method(summary, IPosRanges)
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S3method(summary, IPos)
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S3method(`window<-`, Vector)
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S3method(`window<-`, vector)
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S3method(`window<-`, factor)
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### We also export them thru the export() directive so that (a) they can be
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### called directly, (b) tab-completion on the name of the generic shows them,
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### and (c) methods() doesn't asterisk them.
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export(
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as.data.frame.IPosRanges,
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as.data.frame.IPos,
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diff.AtomicList,
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summary.IPosRanges,
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summary.IPos,
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"window<-.Vector",
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"window<-.vector",
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"window<-.factor"
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)
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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### Export S4 methods for generics NOT defined in this package
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###
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exportMethods(
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## Methods for generics defined in the base package:
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length, "length<-",
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names, "names<-",
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dim,
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dimnames, "dimnames<-",
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"[", "[<-", "[[", "[[<-",
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as.integer,
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as.character,
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as.factor,
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as.matrix,
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drop,
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min, max, range,
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diff,
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transform,
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nchar, chartr, tolower, toupper,
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sub, gsub,
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startsWith, endsWith,
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"split<-",
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"!",
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merge,
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is.na,
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by,
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## Methods for generics defined in the methods package:
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coerce, show,
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Ops, Math, Math2, Summary, Complex,
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## Methods for generics defined in the utils package:
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stack,
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## Methods for generics defined in the stats package:
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mean, var, cov, cor, sd, median, quantile, mad, IQR, smoothEnds, runmed,
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"window<-",
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## Methods for generics defined in the stats4 package:
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summary,
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## Methods for generics defined in the BiocGenerics package:
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nrow, ncol,
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NROW, NCOL,
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rownames, "rownames<-",
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colnames, "colnames<-",
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rbind, cbind,
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unlist, relist, unsplit,
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lapply, tapply,
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as.vector, as.list, as.data.frame,
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which, which.max, which.min,
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pmax, pmin, pmax.int, pmin.int,
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match, duplicated, unique, anyDuplicated,
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is.unsorted, order,
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append,
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paste,
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table,
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union, intersect, setdiff,
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start, "start<-", end, "end<-", width, "width<-", pos,
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dims, nrows, ncols,
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updateObject,
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## Methods for generics defined in the S4Vectors package:
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ROWNAMES, "ROWNAMES<-",
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bindROWS,
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extractROWS, replaceROWS, getListElement,
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parallel_slot_names,
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classNameForDisplay,
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from, to,
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nLnode, nRnode,
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pcompare, pcompareRecursively,
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selfmatch,
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runLength, "runValue<-",
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runsum, runmean, runwtsum, runq,
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elementNROWS, isEmpty,
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revElements,
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as.env,
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active, "active<-"
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)
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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### Export non-generic functions
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###
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export(
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multisplit,
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IRanges, solveUserSEW,
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successiveIRanges,
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slidingIRanges,
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breakInChunks,
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whichAsIRanges,
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asNormalIRanges,
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rangeComparisonCodeToLetter,
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IPos,
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NCList, NCLists,
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H2LGrouping, Dups,
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PartitioningByEnd, PartitioningByWidth, PartitioningMap,
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RangedSelection,
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IRangesList,
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RleViewsList,
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"%over%", "%within%", "%outside%",
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"%pover%", "%pwithin%", "%poutside%",
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mergeByOverlaps, findOverlapPairs,
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MaskCollection.show_frame,
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Mask,
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read.gapMask,
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read.agpMask,
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read.liftMask,
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read.rmMask,
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read.trfMask,
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##read.chain,
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successiveViews, slidingViews,
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LogicalList, IntegerList, NumericList, ComplexList,
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CharacterList, RawList, RleList, FactorList,
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DataFrameList, SplitDataFrameList,
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ManyToOneGrouping, ManyToManyGrouping, regroup,
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heads, tails,
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selectNearest,
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INCOMPATIBLE_ARANGES_MSG, extractListFragments, equisplit
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)
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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### Export S4 generics defined in IRanges, and corresponding methods
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###
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export(
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## range-squeezers.R:
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ranges, rglist,
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## Ranges-and-RangesList-classes.R:
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mid,
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isNormal, whichFirstNotNormal,
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## Views-class.R:
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subject,
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"ranges<-",
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Views,
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trim, subviews,
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viewApply, viewMins, viewMaxs, viewSums, viewMeans,
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viewWhichMins, viewWhichMaxs, viewRangeMins, viewRangeMaxs,
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## Grouping-class.R:
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nobj, grouplengths, members, vmembers, togroup, togrouplength,
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high2low, low2high, grouprank, togrouprank, mapOrder,
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## Rle-class-leftovers.R:
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findRange, splitRanges,
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## extractList.R:
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extractList,
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## DataFrameList-class.R:
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commonColnames, "commonColnames<-",
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columnMetadata, "columnMetadata<-",
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## IntegerRangesList-class.R:
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space,
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## MaskCollection-class.R:
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nir_list,
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desc, "desc<-",
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maskedwidth, maskedratio,
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collapse,
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## findOverlaps-methods.R:
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findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps,
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overlapsRanges,
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poverlaps,
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## windows-methods.R:
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windows, narrow,
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## intra-range-methods.R:
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update_ranges,
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shift, resize, flank, promoters, terminators,
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reflect, restrict, threebands,
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## inter-range-methods.R:
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reduce, gaps, disjoin, isDisjoint, disjointBins,
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## reverse-methods.R:
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reverse,
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## coverage-methods.R:
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coverage,
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## cvg-methods.R:
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cvg,
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## slice-methods.R:
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slice,
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## setops-methods.R:
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punion, pintersect, psetdiff, pgap,
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## nearest-methods.R:
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precede, follow, nearest, distance, distanceToNearest,
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## tile-methods.R:
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tile, slidingWindows,
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## AtomicList-utils.R:
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ifelse2
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)
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### Same list as above.
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exportMethods(
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ranges, rglist,
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runsum, runmean, runwtsum, runq,
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mid,
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isNormal, whichFirstNotNormal,
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subject,
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"ranges<-",
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Views,
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trim, subviews,
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viewApply, viewMins, viewMaxs, viewSums, viewMeans,
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viewWhichMins, viewWhichMaxs, viewRangeMins, viewRangeMaxs,
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nobj, grouplengths, members, vmembers, togroup, togrouplength,
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high2low, low2high, grouprank, togrouprank, mapOrder,
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findRange, splitRanges,
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extractList,
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commonColnames, "commonColnames<-",
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columnMetadata, "columnMetadata<-",
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space,
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nir_list,
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desc, "desc<-",
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maskedwidth, maskedratio,
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collapse,
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findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps,
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overlapsRanges,
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poverlaps,
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windows, narrow,
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update_ranges,
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shift, resize, flank, promoters, terminators,
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reflect, restrict, threebands,
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reduce, gaps, disjoin, isDisjoint, disjointBins,
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reverse,
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coverage,
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cvg,
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slice,
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punion, pintersect, psetdiff, pgap,
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precede, follow, nearest, distance, distanceToNearest,
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tile, slidingWindows,
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ifelse2
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)
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