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}, { "page": "findOverlaps-methods", "title": "Finding overlapping genomic ranges", "topics": [ "countOverlaps", "countOverlaps,GenomicRanges,GenomicRanges-method", "findOverlaps", "findOverlaps,GenomicRanges,GenomicRanges-method", "findOverlaps,GenomicRanges,GRangesList-method", "findOverlaps,GRangesList,GenomicRanges-method", "findOverlaps,GRangesList,GRangesList-method", "findOverlaps-methods", "overlapsAny", "subsetByOverlaps" ] }, { "page": "genomic-range-squeezers", "title": "Squeeze the genomic ranges out of a range-based object", "topics": [ "genomic-range-squeezers", "granges", "grglist", "grglist,Pairs-method" ] }, { "page": "GenomicRanges-comparison", "title": "Comparing and ordering genomic ranges", "topics": [ "duplicated,GenomicRanges-method", "duplicated.GenomicRanges", "GenomicRanges-comparison", "is.unsorted,GenomicRanges-method", "match,GenomicRanges,GenomicRanges-method", "order,GenomicRanges-method", "pcompare", "pcompare,GenomicRanges,GenomicRanges-method", "rank,GenomicRanges-method", "selfmatch,GenomicRanges-method", "sort,GenomicRanges-method", "sort.GenomicRanges" ] }, { "page": "GenomicRangesList-class", "title": "GenomicRangesList objects", "topics": [ "class:CompressedGenomicRangesList", "class:GenomicRangesList", "class:GenomicRanges_OR_GenomicRangesList", "class:SimpleGenomicRangesList", "CompressedGenomicRangesList", "CompressedGenomicRangesList-class", "elementMetadata,GenomicRangesList-method", "elementMetadata<-,CompressedGenomicRangesList-method", "end<-,CompressedGenomicRangesList-method", "extractROWS,GenomicRangesList,ANY-method", "GenomicRangesList", "GenomicRangesList-class", "GenomicRanges_OR_GenomicRangesList", "GenomicRanges_OR_GenomicRangesList-class", "getListElement,GenomicRangesList-method", "length,GenomicRangesList-method", "names,GenomicRangesList-method", "names<-,GenomicRangesList-method", "score,GenomicRangesList-method", "score<-,GenomicRangesList-method", "seqinfo,CompressedGenomicRangesList-method", "seqinfo,GenomicRangesList-method", "seqinfo<-,CompressedGenomicRangesList-method", "seqnames,GenomicRangesList-method", "seqnames<-,CompressedGenomicRangesList-method", "show,GenomicRangesList-method", "SimpleGenomicRangesList", "SimpleGenomicRangesList-class", "start<-,CompressedGenomicRangesList-method", "strand,GenomicRangesList-method", "strand<-,CompressedGenomicRangesList,ANY-method", "strand<-,CompressedGenomicRangesList,character-method", "unlist,GenomicRangesList-method", "updateObject,GenomicRangesList-method", "width<-,CompressedGenomicRangesList-method" ] }, { "page": "genomicvars", "title": "Manipulating genomic variables", "topics": [ "bindAsGRanges", "binnedAverage", "coerce,RleList,GRanges-method", "coerce,RleViewsList,GRanges-method", "genomicvariables", "genomicvars", "mcolAsRleList" ] }, { "page": "GNCList-class", "title": "GNCList objects", "topics": [ "class:GNCList", "coerce,GenomicRanges,GNCList-method", "coerce,GNCList,GRanges-method", "end,GNCList-method", "GNCList", "GNCList-class", "granges,GNCList-method", "length,GNCList-method", "names,GNCList-method", "ranges,GNCList-method", "seqinfo,GNCList-method", "seqnames,GNCList-method", "start,GNCList-method", "strand,GNCList-method", "width,GNCList-method" ] }, { "page": "GPos-class", "title": "Memory-efficient representation of genomic positions", "topics": [ "as.data.frame,GPos-method", "as.data.frame.GPos", "class:GPos", "class:StitchedGPos", "class:UnstitchedGPos", "coerce,ANY,GPos-method", "coerce,ANY,StitchedGPos-method", "coerce,ANY,UnstitchedGPos-method", "coerce,GRanges,GPos-method", "coerce,GRanges,StitchedGPos-method", "coerce,GRanges,UnstitchedGPos-method", "coerce,StitchedGPos,GRanges-method", "coerce,UnstitchedGPos,GRanges-method", "from_GPos_to_GRanges", "GPos", "GPos-class", "pos,GPos-method", "show,GPos-method", "StitchedGPos", "StitchedGPos-class", "summary,GPos-method", "summary.GPos", "UnstitchedGPos", "UnstitchedGPos-class", "updateObject,GPos-method" ] }, { "page": "GRanges-class", "title": "GRanges objects", "topics": [ "$,GenomicRanges-method", "$<-,GenomicRanges-method", "as.character,GenomicRanges-method", "as.data.frame,GenomicRanges-method", "as.data.frame.GenomicRanges", "as.factor,GenomicRanges-method", "bindROWS,GenomicRanges-method", "class:GenomicPos", "class:GenomicRanges", "class:GRanges", "class:IRanges_OR_IPos", "coerce,ANY,GenomicRanges-method", "coerce,character,GRanges-method", "coerce,factor,GRanges-method", "coerce,GenomicRanges,CompressedIRangesList-method", "coerce,GenomicRanges,GRanges-method", "coerce,GenomicRanges,Grouping-method", "coerce,GenomicRanges,IntegerRangesList-method", "coerce,GenomicRanges,IRangesList-method", "coerce,IntegerRangesList,GRanges-method", "coerce,Seqinfo,GRanges-method", "coerce,Seqinfo,IntegerRangesList-method", "end<-,GenomicRanges-method", "GenomicPos", "GenomicPos-class", "GenomicRanges", "GenomicRanges-class", "GenomicRanges_OR_missing-class", "getListElement,GenomicRanges-method", "GRanges", "granges,GenomicRanges-method", "GRanges-class", "IRanges_OR_IPos", "IRanges_OR_IPos-class", "length,GenomicRanges-method", "names,GenomicRanges-method", "names<-,GenomicRanges-method", "parallel_slot_names,GRanges-method", "ranges,GRanges-method", "ranges<-,GenomicRanges-method", "score,GenomicRanges-method", "score<-,GenomicRanges-method", "seqinfo,GRanges-method", "seqinfo,List-method", "seqinfo<-,GenomicRanges-method", "seqinfo<-,List-method", "seqnames,GRanges-method", "seqnames<-,GenomicRanges-method", "show,GenomicRanges-method", "start,GenomicRanges-method", "start<-,GenomicRanges-method", "strand,GRanges-method", "strand<-,GenomicRanges,ANY-method", "summary,GenomicRanges-method", "summary.GenomicRanges", "update,GRanges-method", "updateObject,GRanges-method", "width,GenomicRanges-method", "width<-,GenomicRanges-method", "[,list_OR_List,GenomicRanges-method" ] }, { "page": "GRangesFactor-class", "title": "GRangesFactor objects", "topics": [ "class:GRangesFactor", "coerce,ANY,GRangesFactor-method", "coerce,Factor,GRanges-method", "end,GRangesFactor-method", "FactorToClass,GRanges-method", "granges,GRangesFactor-method", "GRangesFactor", "GRangesFactor-class", "pos,GRangesFactor-method", "ranges,GRangesFactor-method", "seqinfo,GRangesFactor-method", "seqnames,GRangesFactor-method", "show,GRangesFactor-method", "start,GRangesFactor-method", "strand,GRangesFactor-method", "width,GRangesFactor-method" ] }, { "page": "GRangesList-class", "title": "GRangesList objects", "topics": [ "class:CompressedGRangesList", "class:GenomicRanges_OR_GRangesList", "class:GRangesList", "class:SimpleGRangesList", "coerce,CompressedGRangesList,CompressedIRangesList-method", "coerce,CompressedGRangesList,IntegerRangesList-method", "coerce,CompressedGRangesList,IRangesList-method", "coerce,GenomicRangesList,SimpleGRangesList-method", "coerce,List,CompressedGRangesList-method", "coerce,list,CompressedGRangesList-method", "coerce,List,GRangesList-method", "coerce,list,GRangesList-method", "coerce,List,SimpleGRangesList-method", "coerce,list,SimpleGRangesList-method", "coerce,SimpleGenomicRangesList,SimpleGRangesList-method", "coerce,SimpleList,SimpleGRangesList-method", "CompressedGRangesList", "CompressedGRangesList-class", "GenomicRanges_OR_GRangesList", "GenomicRanges_OR_GRangesList-class", "GRangesList", "GRangesList-class", "makeGRangesListFromFeatureFragments", "ranges,CompressedGRangesList-method", "ranges<-,CompressedGRangesList-method", "relistToClass,GRanges-method", "SimpleGRangesList", "SimpleGRangesList-class", "sort,CompressedGRangesList-method", "sort,GRangesList-method", "sort.GRangesList", "[,CompressedGRangesList,ANY-method", "[<-,CompressedGRangesList,ANY,ANY,ANY-method", "[<-,CompressedGRangesList,ANY-method", "[<-,CompressedGRangesList-method" ] }, { "page": "inter-range-methods", "title": "Inter range transformations of a GRanges or GRangesList object", "topics": [ "disjoin", "disjoin,GenomicRanges-method", "disjoin,GRangesList-method", "disjointBins", "disjointBins,GenomicRanges-method", "gaps", "gaps,GenomicRanges-method", "inter-range-methods", "isDisjoint", "isDisjoint,GenomicRanges-method", "isDisjoint,GRangesList-method", "isDisjoint,StitchedGPos-method", "range", "range,GenomicRanges-method", "range,GRangesList-method", "range,StitchedGPos-method", "reduce", "reduce,GenomicRanges-method", "reduce,GRangesList-method" ] }, { "page": "intra-range-methods", "title": "Intra range transformations of a GRanges or GRangesList object", "topics": [ "flank", "flank,GenomicRanges-method", "intra-range-methods", "narrow", "narrow,GenomicRanges-method", "promoters", "promoters,GenomicRanges-method", "resize", "resize,GenomicRanges-method", "restrict", "restrict,GenomicRanges-method", "shift", "shift,GenomicRanges-method", "terminators", "terminators,GenomicRanges-method", "trim", "trim,GenomicRanges-method", "trim,GRangesList-method", "update_ranges,GenomicRanges-method" ] }, { "page": "makeGRangesFromDataFrame", "title": "Make a GRanges object from a data.frame or DataFrame", "topics": [ "coerce,data.frame,GPos-method", "coerce,data.frame,GRanges-method", "coerce,DataFrame,GPos-method", "coerce,DataFrame,GRanges-method", "makeGPosFromDataFrame", "makeGRangesFromDataFrame" ] }, { "page": "makeGRangesListFromDataFrame", "title": "Make a GRangesList object from a data.frame or DataFrame", "topics": [ "makeGRangesListFromDataFrame" ] }, { "page": "nearest-methods", "title": "Finding the nearest genomic range/position neighbor", "topics": [ "distance", "distance,GenomicRanges,GenomicRanges-method", "distanceToNearest", "distanceToNearest,GenomicRanges,GenomicRanges-method", "distanceToNearest,GenomicRanges,missing-method", "follow", "follow,GenomicRanges,GenomicRanges-method", "follow,GenomicRanges,missing-method", "nearest", "nearest,GenomicRanges,GenomicRanges-method", "nearest,GenomicRanges,missing-method", "nearest-methods", "nearestKNeighbors", "nearestKNeighbors,GenomicRanges,GenomicRanges-method", "nearestKNeighbors,GenomicRanges,missing-method", "precede", "precede,GenomicRanges,GenomicRanges-method", "precede,GenomicRanges,missing-method" ] }, { "page": "phicoef", "title": "Calculate the \"phi coefficient\" between two binary variables", "topics": [ "phicoef" ] }, { "page": "setops-methods", "title": "Set operations on genomic ranges", "topics": [ "intersect", "intersect,GenomicRanges,GenomicRanges-method", "intersect,GenomicRanges,Vector-method", "intersect,GRangesList,GRangesList-method", "intersect,Vector,GenomicRanges-method", "pgap", "pgap,GRanges,GRanges-method", "pintersect", "pintersect,GRanges,GRanges-method", "pintersect,GRanges,GRangesList-method", "pintersect,GRangesList,GRanges-method", "psetdiff", "psetdiff,GRanges,GRanges-method", "psetdiff,GRanges,GRangesList-method", "punion", "punion,GRanges,GRanges-method", "punion,GRanges,GRangesList-method", "punion,GRangesList,GRanges-method", "setdiff", "setdiff,GenomicRanges,GenomicRanges-method", "setdiff,GenomicRanges,Vector-method", "setdiff,GRangesList,GRangesList-method", "setdiff,Vector,GenomicRanges-method", "setops-methods", "union", "union,GenomicRanges,GenomicRanges-method", "union,GenomicRanges,Vector-method", "union,GRangesList,GRangesList-method", "union,Vector,GenomicRanges-method" ] }, { "page": "strand-utils", "title": "Strand utilities", "topics": [ "invertStrand,character-method", "invertStrand,factor-method", "invertStrand,integer-method", "invertStrand,logical-method", "invertStrand,NULL-method", "invertStrand,Rle-method", "invertStrand,RleList-method", "strand,character-method", "strand,DataFrame-method", "strand,factor-method", "strand,integer-method", "strand,logical-method", "strand,missing-method", "strand,NULL-method", "strand,Rle-method", "strand,RleList-method", "strand-utils", "strand<-,DataFrame,ANY-method" ] }, { "page": "subtract-methods", "title": "Subtract a set of genomic ranges from a GRanges 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