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"unstrsplit,list-method" ] }, { "page": "DataFrame-class", "title": "DataFrame objects", "topics": [ "as.data.frame,DataFrame-method", "as.data.frame.DataFrame", "as.matrix,DataFrame-method", "class:DataFrame", "class:DFrame", "classNameForDisplay,DFrame-method", "coerce,ANY,DataFrame-method", "coerce,ANY,DataFrame_OR_NULL-method", "coerce,ANY,DFrame-method", "coerce,AsIs,DFrame-method", "coerce,data.frame,DFrame-method", "coerce,data.table,DFrame-method", "coerce,list,DFrame-method", "coerce,NULL,DFrame-method", "coerce,SimpleList,DataFrame-method", "coerce,SimpleList,DFrame-method", "coerce,table,DFrame-method", "coerce,Vector,DFrame-method", "coerce,xtabs,DFrame-method", "colnames,DataFrame-method", "colnames<-,DataFrame-method", "DataFrame", "DataFrame-class", "DFrame", "DFrame-class", "dimnames<-,DataFrame-method", "droplevels,DFrame-method", "extractCOLS,DataFrame-method", "extractROWS,DataFrame,ANY-method", "getListElement,DataFrame-method", 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"merge,data.frame,DataFrame-method", "merge,DataFrame,data.frame-method", "merge,DataFrame,DataFrame-method" ] }, { "page": "DataFrame-comparison", "title": "DataFrame comparison methods", "topics": [ "<=,DataFrame,DataFrame-method", "==,DataFrame,DataFrame-method", "duplicated,DataFrame-method", "duplicated.DataFrame", "match,DataFrame,DataFrame-method", "order,DataFrame-method", "pcompare,DataFrame,DataFrame-method", "sameAsPreviousROW,DataFrame-method", "sort,DataFrame-method", "sort.DataFrame", "unique,DataFrame-method", "unique.DataFrame" ] }, { "page": "DataFrame-utils", "title": "Common operations on DataFrame objects", "topics": [ "complete.cases,DataFrame-method", "DataFrame-utils", "is.na,DataFrame-method", "na.exclude,DataFrame-method", "na.omit,DataFrame-method", "relistToClass,data.frame-method", "relistToClass,DataFrame-method", "transform,DataFrame-method", "transform.DataFrame", "xtabs,DataFrame-method" ] }, { "page": "DataFrameFactor-class", "title": "DataFrameFactor 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"integer_OR_raw-class", "levels", "levels<-", "levels<-,Factor-method", "match,Factor,Factor-method", "names,Factor-method", "names<-,Factor-method", "nlevels", "nlevels,Factor-method", "parallel_slot_names,Factor-method", "pcompare,Factor,Factor-method", "selfmatch,Factor-method", "show,Factor-method", "showAsCell,Factor-method", "unfactor", "unfactor,Factor-method", "unfactor,factor-method", "xtfrm,Factor-method" ] }, { "page": "FilterMatrix-class", "title": "Matrix for Filter Results", "topics": [ "cbind,FilterMatrix-method", "class:FilterMatrix", "FilterMatrix", "FilterMatrix-class", "filterRules", "filterRules,FilterMatrix-method", "rbind,FilterMatrix-method", "show,FilterMatrix-method", "summary,FilterMatrix-method", "[,FilterMatrix-method" ] }, { "page": "FilterRules-class", "title": "Collection of Filter Rules", "topics": [ "&,FilterRules,FilterRules-method", "active", "active,FilterRules-method", "active<-", "active<-,FilterRules-method", "class:expression_OR_function", "class:FilterRules", "coerce,ANY,FilterRules-method", "coerce,function,FilterClosure-method", "coerce,SimpleList,FilterRules-method", "coerce,standardGeneric,FilterClosure-method", "eval,FilterRules,ANY-method", "evalSeparately", "evalSeparately,FilterRules-method", "expression_OR_function", "expression_OR_function-class", "FilterRules", "filterRules,FilterResults-method", "FilterRules-class", "parallel_slot_names,FilterRules-method", "params", "params,FilterClosure-method", "show,FilterClosure-method", "subsetByFilter", "subsetByFilter,ANY,FilterRules-method", "summary,FilterResults-method", "summary,FilterRules-method", "[,FilterRules-method", "[[<-,FilterRules-method" ] }, { "page": "Hits-class", "title": "Hits objects", "topics": [ "as.data.frame,Hits-method", "as.data.frame.Hits", "as.matrix,Hits-method", "as.table,Hits-method", "bindROWS,Hits-method", "breakTies", "class:Hits", "class:SelfHits", "class:SortedByQueryHits", "class:SortedByQuerySelfHits", "classNameForDisplay,SortedByQueryHits-method", "coerce,Hits,DFrame-method", "coerce,Hits,SelfHits-method", "coerce,Hits,SortedByQueryHits-method", "coerce,Hits,SortedByQuerySelfHits-method", "coerce,SelfHits,SortedByQuerySelfHits-method", "coerce,SortedByQueryHits,SortedByQuerySelfHits-method", "countLnodeHits", "countLnodeHits,Hits-method", "countQueryHits", "countRnodeHits", "countRnodeHits,Hits-method", "countSubjectHits", "extractROWS,SortedByQueryHits,ANY-method", "from", "from,Hits-method", "Hits", "Hits-class", "isRedundantHit", "isSelfHit", "makeNakedCharacterMatrixForDisplay,Hits-method", "nLnode", "nLnode,Hits-method", "nnode", "nnode,SelfHits-method", "nRnode", "nRnode,Hits-method", "parallel_slot_names,Hits-method", "queryHits", "queryLength", "remapHits", "selectHits", "SelfHits", "SelfHits-class", "show,Hits-method", "sort,SortedByQueryHits-method", "SortedByQueryHits", "SortedByQueryHits-class", "SortedByQuerySelfHits", "SortedByQuerySelfHits-class", "subjectHits", "subjectLength", "summary,Hits-method", "summary.Hits", "t,Hits-method", "t.Hits", "to", "to,Hits-method", "updateObject,Hits-method" ] }, { "page": "Hits-comparison", "title": "Comparing and ordering hits", "topics": [ "Hits-comparison", "match,Hits,Hits-method", "order,Hits-method", "pcompare,Hits,Hits-method" ] }, { "page": "Hits-setops", "title": "Set operations on Hits objects", "topics": [ "Hits-setops", "union,SortedByQueryHits,Hits-method" ] }, { "page": "HitsList-class", "title": "List of Hits objects", "topics": [ "as.matrix,HitsList-method", "as.table,HitsList-method", "class:HitsList", "class:SelfHitsList", "class:SortedByQueryHitsList", "class:SortedByQuerySelfHitsList", "coerce,HitsList,SortedByQueryHitsList-method", "coerce,SortedByQueryHitsList,HitsList-method", "from,HitsList-method", "HitsList", "HitsList-class", "queryHits,HitsList-method", "relistToClass,Hits-method", "relistToClass,SortedByQueryHits-method", "SelfHitsList", "SelfHitsList-class", "SortedByQueryHitsList", "SortedByQueryHitsList-class", "SortedByQuerySelfHitsList", "SortedByQuerySelfHitsList-class", "space", "space,HitsList-method", "splitAsList,SortedByQueryHits,ANY-method", "subjectHits,HitsList-method", "t,HitsList-method", "t.HitsList", "to,HitsList-method" ] }, { "page": "integer-utils", "title": "Some utility functions to operate on integer vectors", "topics": [ "duplicatedIntegerPairs", "duplicatedIntegerQuads", "isSequence", "matchIntegerPairs", "matchIntegerQuads", "orderIntegerPairs", "orderIntegerQuads", "selfmatchIntegerPairs", "selfmatchIntegerQuads", "toListOfIntegerVectors" ] }, { "page": "isSorted", "title": "Test if a vector-like object is sorted", "topics": [ "isConstant", "isConstant,array-method", "isConstant,integer-method", "isConstant,numeric-method", "isSorted", "isSorted,ANY-method", "isStrictlySorted", "isStrictlySorted,ANY-method" ] }, { "page": "List-class", "title": "List objects", "topics": [ "$,List-method", "$<-,List-method", "anyNA,List-method", "as.data.frame,List-method", "as.list,List-method", "class:List", "class:list_OR_List", "coerce,ANY,List-method", "coerce,integer,List-method", "coerce,List,list-method", "elementNROWS", "elementNROWS,ANY-method", "elementNROWS,List-method", "elementType", "elementType,List-method", "elementType,vector-method", "getListElement,List-method", "is.na,List-method", "isEmpty", "isEmpty,ANY-method", "isEmpty,List-method", "List", "List-class", "list_OR_List", "list_OR_List-class", "normalizeSingleBracketReplacementValue,List-method", "parallelVectorNames,List-method", "setListElement,List-method", "show,List-method", "showAsCell,List-method", "unlist,List-method", "[,List-method", "[<-,List-method", "[[,List-method", "[[<-,List-method" ] }, { "page": "List-comparison", "title": "Compare and order list-like objects", "topics": [ "<=,List,List-method", "<=,List,list-method", "<=,list,List-method", "==,List,List-method", "==,List,list-method", "==,list,List-method", "duplicated,List-method", "is.unsorted,List-method", "List-comparison", "match,List,List-method", "match,List,list-method", "match,list,List-method", "match,List,Vector-method", "match,List,vector-method", "order,List-method", "pcompare,List,List-method", "pcompare,List,list-method", "pcompare,list,List-method", "pcompareRecursively", "pcompareRecursively,List-method", "pcompareRecursively,list-method", "rank,List-method", "sort,List-method", "sort.List", "unique,List-method", "unique,SimpleList-method" ] }, { "page": "List-utils", "title": "Common operations on List objects", "topics": [ "!,List-method", "cbind,List-method", "cbind.List", "do.call,ANY,List-method", "droplevels,List-method", "droplevels.List", "endoapply", "Filter,List-method", "Find,List-method", "lapply,List-method", "List-utils", "Map,List-method", "mendoapply", "pc", "Position,List-method", "rbind,List-method", "Reduce,List-method", "revElements", "revElements,List-method", "revElements,list-method", "sapply,List-method", "within,List-method" ] }, { "page": "LLint-class", "title": "LLint vectors", "topics": [ "as.character,LLint-method", "as.character.LLint", "as.integer,LLint-method", "as.integer.LLint", "as.LLint", "as.logical,LLint-method", "as.logical.LLint", "as.numeric,LLint-method", "as.numeric.LLint", "bindROWS,LLint-method", "c,LLint-method", "class:integer_OR_LLint", "class:LLint", "coerce,character,LLint-method", "coerce,integer,LLint-method", "coerce,logical,LLint-method", "coerce,numeric,LLint-method", "extractROWS,LLint,ANY-method", "extractROWS,LLint,NSBS-method", "extractROWS,LLint,RangeNSBS-method", "head,LLint-method", "head.LLint", "integer_OR_LLint", "integer_OR_LLint-class", "is.LLint", "is.na,LLint-method", "length,LLint-method", "LLint", "LLint-class", "NA_LLint_", "Ops,LLint,LLint-method", "Ops,LLint,numeric-method", "Ops,numeric,LLint-method", "rep.int,LLint-method", "show,LLint-method", "showAsCell,LLint-method", "Summary,LLint-method", "tail,LLint-method", "tail.LLint", "window,LLint-method", "window.LLint", "[,LLint-method" ] }, { "page": "Pairs-class", "title": "Pairs objects", "topics": [ "as.data.frame,Pairs-method", "class:Pairs", "coerce,list_OR_List,Pairs-method", "coerce,Pairs,DFrame-method", "first", "first,Pairs-method", "first<-", "first<-,Pairs-method", "makeNakedCharacterMatrixForDisplay,Pairs-method", "match,Pairs,Pairs-method", "names,Pairs-method", "names<-,Pairs-method", "order,Pairs-method", "Pairs", "Pairs-class", "parallel_slot_names,Pairs-method", "pcompare,Pairs,Pairs-method", "sameAsPreviousROW,Pairs-method", "second", "second,Pairs-method", "second<-", "second<-,Pairs-method", "show,Pairs-method", "t,Pairs-method", "zipup,Pairs,missing-method" ] }, { "page": "RectangularData-class", "title": "RectangularData objects", "topics": [ "cbind,RectangularData-method", "cbind.RectangularData", "class:RectangularData", "combineCols", "combineRows", "combineUniqueCols", "dim,RectangularData-method", "dimnames,RectangularData-method", "dimnames<-,RectangularData-method", "head,RectangularData-method", "head.RectangularData", "horizontal_slot_names", "rbind,RectangularData-method", "rbind.RectangularData", "RectangularData", "RectangularData-class", "ROWNAMES", "ROWNAMES,ANY-method", "ROWNAMES,RectangularData-method", "ROWNAMES<-", "ROWNAMES<-,ANY-method", "ROWNAMES<-,RectangularData-method", "subset,RectangularData-method", "tail,RectangularData-method", "tail.RectangularData", "vertical_slot_names" ] }, { "page": "Rle-class", "title": "Rle objects", "topics": [ "%in%,Rle,ANY-method", "anyDuplicated,Rle-method", "anyDuplicated,RleNSBS-method", "anyDuplicated.Rle", "anyNA,Rle-method", "append,Rle,vector-method", "append,vector,Rle-method", "as.data.frame,Rle-method", "as.factor,Rle-method", "as.integer,RleNSBS-method", "as.list,Rle-method", "as.list.Rle", "as.vector,Rle-method", "as.vector.Rle", "bindROWS,Rle-method", "class:Rle", "coerce,ANY,Rle-method", "coerce,Rle,character-method", "coerce,Rle,complex-method", "coerce,Rle,factor-method", "coerce,Rle,integer-method", "coerce,Rle,list-method", "coerce,Rle,logical-method", "coerce,Rle,numeric-method", "coerce,Rle,raw-method", "coerce,Rle,vector-method", "decode", "decode,ANY-method", "decode,Rle-method", "duplicated,Rle-method", "end,Rle-method", "extractROWS,Rle,ANY-method", "extractROWS,Rle,NSBS-method", "extractROWS,Rle,RangeNSBS-method", "extractROWS,Rle,RleNSBS-method", "findRun", "findRun,Rle-method", "intersect,ANY,Rle-method", "intersect,Rle,ANY-method", "intersect,Rle,Rle-method", "is.finite,Rle-method", "is.na,Rle-method", "is.unsorted,Rle-method", "isStrictlySorted,Rle-method", "isStrictlySorted,RleNSBS-method", "length,Rle-method", "length,RleNSBS-method", "match,ANY,Rle-method", "match,Rle,ANY-method", "match,Rle,Rle-method", "nrun", "nrun,Rle-method", "NSBS,Rle-method", "order,Rle-method", "rank,Rle-method", "rep,Rle-method", "rep.int,Rle-method", "replaceROWS,Rle,ANY-method", "replaceROWS,Rle-method", "rev,Rle-method", "rev.Rle", "Rle", "Rle,ANY-method", "Rle,Rle-method", "Rle-class", "runLength", "runLength,Rle-method", "runLength<-", "runLength<-,Rle-method", "runValue", "runValue,Rle-method", "runValue<-", "runValue<-,Rle-method", "setdiff,ANY,Rle-method", "setdiff,Rle,ANY-method", "setdiff,Rle,Rle-method", "show,Rle-method", "sort,Rle-method", "sort.Rle", "start,Rle-method", "table,Rle-method", "tabulate,Rle-method", "union,ANY,Rle-method", "union,Rle,ANY-method", "union,Rle,Rle-method", "unique,Rle-method", "width,Rle-method", "xtfrm,Rle-method", "[,Rle-method", "[<-,Rle,ANY-method", "[<-,Rle-method" ] }, { "page": "Rle-runstat", "title": "Fixed-width running window summaries", "topics": [ "Rle-runstat", "runmean", "runmean,Rle-method", "runmed,Rle-method", "runq", "runq,Rle-method", "runsum", "runsum,Rle-method", "runwtsum", "runwtsum,Rle-method", "smoothEnds,Rle-method" ] }, { "page": "Rle-utils", "title": "Common operations on Rle objects", "topics": [ "!,Rle-method", "chartr,ANY,ANY,Rle-method", "Complex,Rle-method", "cor,Rle,Rle-method", "cov,Rle,Rle-method", "diff,Rle-method", "diff.Rle", "droplevels,Rle-method", "droplevels.Rle", "grep,ANY,Rle-method", "grepl,ANY,Rle-method", "gsub,ANY,ANY,Rle-method", "IQR,Rle-method", "levels,Rle-method", "levels.Rle", "levels<-,Rle-method", "mad,Rle-method", "mad.Rle", "Math,Rle-method", "Math2,Rle-method", "mean,Rle-method", "mean.Rle", "median,Rle-method", "median.Rle", "nchar,Rle-method", "Ops,Rle,Rle-method", "Ops,Rle,vector-method", "Ops,vector,Rle-method", "paste,Rle-method", "pmax,Rle-method", "pmax.int,Rle-method", "pmin,Rle-method", "pmin.int,Rle-method", "quantile,Rle-method", "quantile.Rle", "Rle-utils", "sd,Rle-method", "sub,ANY,ANY,Rle-method", "substr,Rle-method", "substring,Rle-method", "Summary,Rle-method", "summary,Rle-method", "summary.Rle", "tolower,Rle-method", "toupper,Rle-method", "var,Rle,missing-method", "var,Rle,Rle-method", "which,Rle-method", "which.max,Rle-method" ] }, { "page": "shiftApply-methods", "title": "Apply a function over subsequences of 2 vector-like objects", "topics": [ "shiftApply", "shiftApply,Vector,Vector-method", "shiftApply,vector,vector-method", "shiftApply-methods" ] }, { "page": "show-utils", "title": "Display utilities", "topics": [ "cbind_mcols_for_display", "classNameForDisplay", "classNameForDisplay,ANY-method", "coolcat", "get_showHeadLines", "get_showTailLines", "makeClassinfoRowForCompactPrinting", "makeNakedCharacterMatrixForDisplay", "makeNakedCharacterMatrixForDisplay,ANY-method", "makePrettyMatrixForCompactPrinting", "printAtomicVectorInAGrid", "set_showHeadLines", "set_showTailLines", "show-utils", "showAsCell", "showAsCell,ANY-method", "showAsCell,AsIs-method", "showAsCell,character-method", "showAsCell,data.frame-method", "showAsCell,list-method", "showAsCell,numeric-method", "showHeadLines", "showTailLines" ] }, { "page": "SimpleList-class", "title": "SimpleList objects", "topics": [ "as.env,SimpleList-method", "as.list,SimpleList-method", "as.list.SimpleList", "class:SimpleList", "classNameForDisplay,SimpleList-method", "coerce,ANY,SimpleList-method", "coerce,list,List-method", "getListElement,SimpleList-method", "lapply,SimpleList-method", "names,SimpleList-method", "names<-,SimpleList-method", "parallel_slot_names,SimpleList-method", "SimpleList", "SimpleList-class", "updateObject,SimpleList-method" ] }, { "page": "splitAsList", "title": "Divide a vector-like object into groups", "topics": [ "relistToClass", "relistToClass,ANY-method", "split", "split,ANY,Vector-method", "split,list,Vector-method", "split,Vector,ANY-method", "split,Vector,Vector-method", "splitAsList", "splitAsList,ANY,ANY-method", "splitAsList,ANY-method", "splitAsList,SortedByQueryHits-method" ] }, { "page": "stack-methods", "title": "Stack objects", "topics": [ "mstack", "mstack,DataFrame-method", "mstack,Vector-method", "mstack,vector-method", "stack,List-method", "stack,matrix-method", "stack-methods" ] }, { "page": "subsetting-utils", "title": "Subsetting utilities", "topics": [ "anyDuplicated,NSBS-method", "anyDuplicated,RangeNSBS-method", "anyDuplicated.NSBS", "as.integer,NativeNSBS-method", "as.integer,RangeNSBS-method", "class:NSBS", "extractCOLS", "extractROWS", "extractROWS,ANY,ANY-method", "extractROWS,array,RangeNSBS-method", "extractROWS,data.frame,RangeNSBS-method", "extractROWS,vector_OR_factor,RangeNSBS-method", "getListElement", "getListElement,list-method", "isStrictlySorted,NSBS-method", "isStrictlySorted,RangeNSBS-method", "length,NSBS-method", "length,RangeNSBS-method", "max,NSBS-method", "max,RangeNSBS-method", "mergeROWS", "mergeROWS,ANY,ANY-method", "normalizeDoubleBracketSubscript", "normalizeSingleBracketReplacementValue", "normalizeSingleBracketReplacementValue,ANY-method", "normalizeSingleBracketSubscript", "NSBS", "NSBS,ANY-method", "NSBS,character-method", "NSBS,factor-method", "NSBS,logical-method", 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