522 lines
11 KiB
Plaintext
522 lines
11 KiB
Plaintext
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useDynLib(S4Vectors)
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import(methods)
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importFrom(utils, head, tail, head.matrix, tail.matrix, getS3method, stack)
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importFrom(stats, cov, cor, median, quantile,
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smoothEnds, runmed, window, "window<-", aggregate,
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na.omit, na.exclude, complete.cases, setNames, terms)
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importFrom(stats4, summary, update)
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import(BiocGenerics)
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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### Export S4 classes
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###
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exportClasses(
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character_OR_NULL, vector_OR_factor, atomic,
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LLint, integer_OR_LLint,
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RectangularData,
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NSBS,
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Annotated,
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DataFrame_OR_NULL,
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Vector, vector_OR_Vector,
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Hits, SelfHits, SortedByQueryHits, SortedByQuerySelfHits,
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Rle,
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integer_OR_raw, Factor,
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List, list_OR_List,
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SimpleList,
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HitsList, SortedByQueryHitsList,
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DataFrame, DFrame,
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DataFrameFactor,
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TransposedDataFrame,
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Pairs,
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expression_OR_function, FilterRules, FilterMatrix
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)
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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### Export S3 methods
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###
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S3method(aggregate, Vector)
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S3method(anyDuplicated, NSBS)
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S3method(anyDuplicated, Vector)
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S3method(anyDuplicated, Rle)
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S3method(as.character, LLint)
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S3method(as.data.frame, DataFrame)
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S3method(as.data.frame, Vector)
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S3method(as.data.frame, Hits)
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S3method(as.integer, LLint)
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S3method(as.list, Rle)
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S3method(as.list, SimpleList)
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S3method(as.list, TransposedDataFrame)
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S3method(as.list, Vector)
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S3method(as.logical, LLint)
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S3method(as.matrix, Vector)
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S3method(as.numeric, LLint)
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S3method(as.vector, Rle)
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S3method(cbind, RectangularData)
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S3method(cbind, List)
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S3method(cbind, DataFrame)
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S3method(diff, Rle)
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S3method(droplevels, Rle)
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S3method(droplevels, Factor)
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S3method(droplevels, List)
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S3method(duplicated, Vector)
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S3method(duplicated, DataFrame)
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S3method(head, LLint)
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S3method(head, RectangularData)
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S3method(head, Vector)
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S3method(intersect, Vector)
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S3method(levels, Rle)
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S3method(mean, Rle)
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S3method(median, Rle)
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S3method(quantile, Rle)
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S3method(rbind, RectangularData)
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S3method(rev, Vector)
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S3method(rev, Rle)
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S3method(setdiff, Vector)
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S3method(setequal, Vector)
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S3method(sort, Vector)
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S3method(sort, Rle)
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S3method(sort, List)
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S3method(sort, DataFrame)
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S3method(subset, Vector)
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S3method(summary, Vector)
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S3method(summary, Hits)
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S3method(summary, Rle)
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S3method(t, Hits)
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S3method(t, HitsList)
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S3method(t, DataFrame)
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S3method(t, TransposedDataFrame)
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S3method(tail, LLint)
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S3method(tail, RectangularData)
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S3method(tail, Vector)
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S3method(transform, Vector)
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S3method(transform, DataFrame)
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S3method(union, Vector)
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S3method(unique, Vector)
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S3method(unique, DataFrame)
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S3method(window, LLint)
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S3method(window, Vector)
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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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aggregate.Vector,
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anyDuplicated.NSBS,
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anyDuplicated.Vector,
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anyDuplicated.Rle,
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as.character.LLint,
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as.data.frame.DataFrame,
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as.data.frame.Vector,
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as.data.frame.Hits,
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as.integer.LLint,
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as.list.Rle,
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as.list.SimpleList,
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as.list.TransposedDataFrame,
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as.list.Vector,
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as.logical.LLint,
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as.matrix.Vector,
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as.numeric.LLint,
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as.vector.Rle,
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cbind.RectangularData,
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cbind.List,
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cbind.DataFrame,
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diff.Rle,
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droplevels.Rle,
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droplevels.Factor,
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droplevels.List,
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duplicated.Vector,
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duplicated.DataFrame,
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head.LLint,
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head.RectangularData,
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head.Vector,
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intersect.Vector,
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levels.Rle,
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mean.Rle,
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median.Rle,
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quantile.Rle,
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rbind.RectangularData,
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rev.Vector,
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rev.Rle,
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setdiff.Vector,
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setequal.Vector,
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sort.Vector,
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sort.Rle,
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sort.List,
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sort.DataFrame,
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subset.Vector,
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summary.Vector,
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summary.Hits,
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summary.Rle,
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t.Hits,
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t.HitsList,
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t.DataFrame,
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t.TransposedDataFrame,
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tail.LLint,
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tail.RectangularData,
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tail.Vector,
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transform.Vector,
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transform.DataFrame,
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union.Vector,
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unique.Vector,
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unique.DataFrame,
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window.LLint,
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window.Vector
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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, names, "names<-",
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dim, nrow, ncol,
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dimnames, "dimnames<-",
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is.na, anyNA,
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as.logical, as.integer, as.numeric,
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as.complex, as.character, as.raw, as.factor,
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as.list, as.data.frame,
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as.matrix, as.table,
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"[", "[<-",
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subset, rev, rep, rep.int,
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c, append,
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"==", "!=", "<=", ">=", "<", ">",
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"Ops", "Summary",
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"!",
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match, duplicated, unique, anyDuplicated, "%in%",
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order, sort, is.unsorted, rank, xtfrm,
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merge,
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t,
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by,
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nchar, substr, substring, levels, "levels<-", droplevels,
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"[[", "[[<-", "$", "$<-",
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lengths,
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split,
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eval, with, within,
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expand.grid,
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## Methods for generics defined in the methods package:
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coerce, show,
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## Methods for generics defined in the utils package:
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head, tail, stack,
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## Methods for generics defined in the stats package:
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var, cov, cor, sd, window, aggregate, na.omit, na.exclude, complete.cases,
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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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rownames, "rownames<-",
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colnames, "colnames<-",
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rbind, cbind,
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lapply, sapply,
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Reduce, Filter,
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unlist, unname,
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do.call,
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union, intersect, setdiff, setequal,
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xtabs,
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start, end, width,
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grep, grepl,
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updateObject
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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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## S4-utils.R:
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I, setValidity2, new2, setMethods,
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## show-utils.R:
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coolcat,
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get_showHeadLines, set_showHeadLines,
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get_showTailLines, set_showTailLines,
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printAtomicVectorInAGrid,
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cbind_mcols_for_display,
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makePrettyMatrixForCompactPrinting,
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makeClassinfoRowForCompactPrinting,
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## utils.R:
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wmsg,
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.Call2,
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## normarg-utils.R:
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isTRUEorFALSE, isSingleInteger, isSingleNumber, isSingleString,
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isSingleNumberOrNA, isSingleStringOrNA,
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recycleIntegerArg, recycleNumericArg,
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recycleLogicalArg, recycleCharacterArg,
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recycleArg,
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fold,
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## LLint-class.R:
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is.LLint, as.LLint, LLint,
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## subsetting-utils.R:
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normalizeSingleBracketSubscript,
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normalizeDoubleBracketSubscript,
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## integer-utils.R:
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isSequence,
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toListOfIntegerVectors,
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orderIntegerPairs,
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matchIntegerPairs, selfmatchIntegerPairs, duplicatedIntegerPairs,
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orderIntegerQuads,
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matchIntegerQuads, selfmatchIntegerQuads, duplicatedIntegerQuads,
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## character-utils.R:
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safeExplode,
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svn.time,
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## RectangularData-class.R:
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combineUniqueCols,
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## Hits-class.R:
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queryHits, subjectHits,
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queryLength, subjectLength,
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countQueryHits, countSubjectHits,
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Hits, SelfHits,
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selectHits,
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breakTies,
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remapHits,
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isSelfHit,
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isRedundantHit,
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## Factor-class.R:
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Factor,
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## List-class.R:
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List, pc,
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## List-utils.R:
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endoapply, mendoapply,
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## SimpleList-class.R:
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SimpleList,
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## HitsList-class.R:
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HitsList,
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## DataFrame-class.R:
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DataFrame, make_zero_col_DFrame,
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## DataFrameFactor-class:
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DataFrameFactor,
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## Pairs-class.R:
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Pairs,
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## FilterRules-class.R:
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FilterRules, FilterMatrix
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)
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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### Export S4 generics defined in S4Vectors, and corresponding methods
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###
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export(
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## show-utils.R:
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classNameForDisplay, showAsCell, makeNakedCharacterMatrixForDisplay,
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## bindROWS.R:
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bindROWS, bindCOLS,
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## isSorted.R:
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isConstant, isSorted, isStrictlySorted,
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## subsetting-utils.R:
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NSBS,
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normalizeSingleBracketReplacementValue,
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extractROWS, replaceROWS, mergeROWS, extractCOLS, replaceCOLS,
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getListElement, setListElement,
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## character-utils.R:
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unstrsplit,
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## RectangularData-class.R:
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vertical_slot_names, horizontal_slot_names,
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ROWNAMES, "ROWNAMES<-",
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combineRows, combineCols,
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## Annotated-class.R:
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metadata, "metadata<-",
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## Vector-class.R:
|
||
|
|
parallel_slot_names, parallelVectorNames,
|
||
|
|
elementMetadata, mcols, values,
|
||
|
|
"elementMetadata<-", "mcols<-", "values<-",
|
||
|
|
rename,
|
||
|
|
as.env,
|
||
|
|
|
||
|
|
## Vector-comparison.R:
|
||
|
|
pcompare,
|
||
|
|
sameAsPreviousROW,
|
||
|
|
selfmatch,
|
||
|
|
findMatches, countMatches,
|
||
|
|
|
||
|
|
## Hits-class.R:
|
||
|
|
from, to, nLnode, nRnode, nnode, countLnodeHits, countRnodeHits,
|
||
|
|
|
||
|
|
## Rle-class.R:
|
||
|
|
runLength, "runLength<-", runValue, "runValue<-", nrun,
|
||
|
|
Rle,
|
||
|
|
findRun, decode,
|
||
|
|
|
||
|
|
## Rle-utils.R:
|
||
|
|
runsum, runmean, runwtsum, runq,
|
||
|
|
|
||
|
|
## Factor-class.R:
|
||
|
|
FactorToClass, unfactor,
|
||
|
|
|
||
|
|
## List-class.R:
|
||
|
|
elementType, elementNROWS, isEmpty,
|
||
|
|
|
||
|
|
## List-comparison.R:
|
||
|
|
pcompareRecursively,
|
||
|
|
|
||
|
|
## splitAsList.R:
|
||
|
|
relistToClass, splitAsList,
|
||
|
|
|
||
|
|
## List-utils.R:
|
||
|
|
revElements,
|
||
|
|
|
||
|
|
## HitsList-class.R:
|
||
|
|
space,
|
||
|
|
|
||
|
|
## DataFrame-utils.R:
|
||
|
|
transform,
|
||
|
|
|
||
|
|
## Pairs-class.R:
|
||
|
|
first, "first<-", second, "second<-", zipup, zipdown,
|
||
|
|
|
||
|
|
## FilterRules-class.R:
|
||
|
|
active, "active<-", evalSeparately, subsetByFilter, params, filterRules,
|
||
|
|
|
||
|
|
## mstack-methods.R
|
||
|
|
mstack,
|
||
|
|
|
||
|
|
## expand-methods.R
|
||
|
|
expand,
|
||
|
|
|
||
|
|
## shiftApply-methods.R:
|
||
|
|
shiftApply
|
||
|
|
)
|
||
|
|
|
||
|
|
### Exactly the same list as above.
|
||
|
|
exportMethods(
|
||
|
|
classNameForDisplay, showAsCell, makeNakedCharacterMatrixForDisplay,
|
||
|
|
bindROWS, bindCOLS,
|
||
|
|
isConstant, isSorted, isStrictlySorted,
|
||
|
|
NSBS,
|
||
|
|
normalizeSingleBracketReplacementValue,
|
||
|
|
extractROWS, replaceROWS,
|
||
|
|
getListElement, setListElement,
|
||
|
|
unstrsplit,
|
||
|
|
vertical_slot_names, horizontal_slot_names,
|
||
|
|
ROWNAMES, "ROWNAMES<-",
|
||
|
|
combineRows, combineCols,
|
||
|
|
metadata, "metadata<-",
|
||
|
|
parallel_slot_names, parallelVectorNames,
|
||
|
|
elementMetadata, mcols, values,
|
||
|
|
"elementMetadata<-", "mcols<-", "values<-",
|
||
|
|
rename,
|
||
|
|
as.env,
|
||
|
|
pcompare,
|
||
|
|
sameAsPreviousROW,
|
||
|
|
selfmatch,
|
||
|
|
findMatches, countMatches,
|
||
|
|
from, to, nLnode, nRnode, nnode, countLnodeHits, countRnodeHits,
|
||
|
|
runLength, "runLength<-", runValue, "runValue<-", nrun,
|
||
|
|
Rle,
|
||
|
|
findRun,
|
||
|
|
runsum, runmean, runwtsum, runq,
|
||
|
|
FactorToClass, unfactor,
|
||
|
|
elementType, elementNROWS, isEmpty,
|
||
|
|
pcompareRecursively,
|
||
|
|
relistToClass, splitAsList,
|
||
|
|
revElements,
|
||
|
|
space,
|
||
|
|
transform,
|
||
|
|
first, "first<-", second, "second<-", zipup, zipdown,
|
||
|
|
active, "active<-", evalSeparately, subsetByFilter, params, filterRules,
|
||
|
|
mstack,
|
||
|
|
expand,
|
||
|
|
shiftApply
|
||
|
|
)
|
||
|
|
|