Function reference • gGnome

All functions
`Junction class constructor` `Junction`	set
`Junction`	Junction
`%^%`(<Junction>)	Junction over
`%&%`(<Junction>)	subset gEdge on overlaps
`amp()`	Amplifications
`balance()`	balance gGnome graphs
`bcheck()`	bcheck
`binstats()`	binstats
`c(<gNode>)` `c(<gEdge>)` `c(<Junction>)` `c(<gWalk>)`	c.gNode
`c(<gGraph>)`	c.gGraph
`cbind()`	cbind wrapper
`chromoplexy()`	Find Chromoplexy chains
`chromothripsis()`	Find Chromothripsis
`colnames2()` `colnames2()`	robust colnames gives back character vector same number of columns of input regardless whether named or not
`copy3()` `copy3()`	make deep copy, recursively useful for dev makes deep copy of R6 object, S4 object, or anything else really
`cougar2gg()`	cougar2gg
`dedup.cols()` `dedup.cols()`	applies dedup to colnames dedup the column names of a data.frame/data.table
`del()`	Find simple deletions and rigmas
`dim(<gGraph>)`	dim
`dt_na2false()` `dt_na2false()`	convert columns with NA to false coerce NA in columns of class "logical" to FALSE
`dup()`	Find duplications and pyrgos
`duped()` `duped()`	duped
`duplicated.matrix()`	R-3.5.1 version of duplicated.matrix
`isNA()`	data table-ize list elements and add name column
`==`(<gGraph>)	equals.gGraph
`events()`	Events calling
`events.to.gr()`	Events to GRanges
`fitcn()`	fitcn
`fusions()`	find fusions
`gEdge`	gEdge
`%&%`(<gEdge>)	subset gEdge on overlaps
`%^%`(<gEdge>)	gEdge over
`gG()`	create gGraph
`gGnome` `gGnome-package`	gGnome
`gGnome.js()`	Generate a gGnome.js instance
`gGraph constructor` `gGraph`	simplify
`gGraph`	gGraph
`%&%`(<gGraph>)	subset gGraph on overlaps
`%^%`(<gNode>)	subset gNode on overlaps
`%&%`(<gNode>)	subset gNode on overlaps
`gNode`	gNode
`gNode.loose()`	gNode.loose
`gW()`	create gWalk
`gWalk`	gWalk
`%^%`(<gWalk>)	subset gWalk on overlaps
`%&%`(<gWalk>)	sets metadata of gWalk object (accessible through $dt accessor)
`gdist()`	gdist
`gr.noval()` `gr.noval()`	get rid of mcols on GRanges/GRangesLists
`gr.spreduce()` `gr.spreduce()`	reduce based on a field(s) to split by in elementMetadata of GRanges, or given vector
`%K%`	similar to setkey except a general use utility slower version of setkey, but for interactive use
`haplograph()`	haplograph
`initialize` `gNode`	copy
`Rcplex2()`	Rcplex2
`intersect.Junction()`	intersect.Junction
`intersect.gEdge()`	intersect.gEdge
`intersect.gNode()`	intersect.gNode
`isNA()`	is.na but also tests for "NA" character
`jJ()`	parse junctions from a variety of formats
`karyotype()`	karyotype
`label.runs()`	label.runs
`length(<gNode>)` `length(<gEdge>)` `length(<Junction>)` `length(<gGraph>)` `length(<gWalk>)` `length(<gNode>)` `length(<gEdge>)`	length.gNode
`lengths()` `lengths.gWalk()`	lengths
`loosefix()`	loosefix
`match3()` `match3()`	similar to setkey except a general use utility very slow version of keying a la data.table but for general/interactive use
`merge(<Junction>)`	merge junctions by overlaps with padding Merges a set of junctions and keeps "seen.by" metadata of junction origin using the argument names to this function If cartesian = TRUE, can only merge a pair of junction objects but then the output contains the overlapping junctions and metadata annotated with a $query.id (index into first argument) and $subject.id (index to into second argument) with deduped outputs,
`merge()`	merge for undefined number of Junction objects
`merge(<repl>)` `merge(<repl>)`	merging data tables with collapsing columns with the same name Merge two data tables with various replacing strategies for columns common between x and y that are not used to merge (i.e. not specified in the "by" argument)
`microhomology()`	get microhomology
`na2false()` `na2false()`	replace logical vector with NA to FALSE
`peel()`	peel
`pgv()`	Generate a PGV instance
`phased.binstats.legacy()`	phased.binstats
`ploidy()`	ploidy Computes ploidy i.e. average CN for a gGraph
`proximity()`	Proximity analysis of two genomic regions and rearrangment movement
`ra.duplicated()`	ra.duplicated
`ra.merge()`	Merges rearrangements represented by `GRangesList` objects
`rand.string()` `rand.string()`	make a random string
`read.juncs()`	read.juncs
`read_cmap()`	read_cmap
`read_xmap()`	read_xmap
`reciprocal()`	Get reciprical connected junctions
`refresh()`	refresh
`rel2abs()`	rel2abs
`rep_len2()` `rep_len2()`	recycle vector along length OR nrow of object
`rleseq()` `rleseq()`	numbers up within repeating elements of a vector
`rowMaxs()` `rowMaxs()`	rowMaxs hack
`rowMins()` `rowMins()`	rowMins hack
`run_gurobi()`	run_gurobi
`seq_along2()` `seq_along2()`	seq along either row of table or length of vector
`seqinfo(<gGraph>)` `seqinfo(<gNode>)` `seqinfo(<gEdge>)` `seqinfo(<Junction>)` `seqinfo(<gWalk>)`	seqinfo
`seqlengths(<gGraph>)` `seqlengths(<gNode>)` `seqlengths(<gEdge>)` `seqlengths(<Junction>)` `seqlengths(<gWalk>)`	seqlengths
`seqlevels(<gGraph>)`	seqlevels
`setcols()` `setcols()`	convenience function to set columns sets columns of an object
`setdiff(<gNode>,<gNode>)` `setdiff(<gEdge>,<gEdge>)` `setdiff(<Junction>,<Junction>)`	setdiff.gNode
`setxor()`	setxor
`simple()`	Simple Event Calling
`sparse_subset()`	sparse_subset
`split.gGraph()`	split.gGraph
`spmelt()`	spMelt
`[`(<Junction>)	Junction
`[`(<gEdge>)	gEdge
`[`(<gNode>)	gNode
`[`(<gWalk>)	gWalk
`sum(<gGraph>)`	sum.gGraph
`tic()`	Find templated insertion chains (tics)
`transplant()`	transplant donor subggraph into recipient
`union(<gNode>,<gNode>)` `union(<gEdge>,<gEdge>)` `union(<Junction>,<Junction>)`	union.gNode
`unique(<Junction>)`	unique.Junction
`width(<gWalk>)` `width(<gNode>)`	width

Reference

All functions