Man pages for mskilab/gGnome
gGnome: reference based assembly graph for analyzing rearranged genomes
| amp | Amplifications |
| balance | balance gGnome graphs |
| bcheck | bcheck |
| binstats | binstats |
| c | c.gNode |
| cbind | cbind wrapper |
| c.gGraph | c.gGraph |
| chromoplexy | Find Chromoplexy chains |
| chromothripsis | Find Chromothripsis |
| colnames2 | robust colnames gives back character vector same number of... |
| convertEdges | convertEdges |
| copy3 | make deep copy, recursively useful for dev makes deep copy of... |
| cougar2gg | cougar2gg |
| dedup.cols | applies dedup to colnames dedup the column names of a... |
| del | Find simple deletions and rigmas |
| dim | dim |
| dt_na2false | convert columns with NA to false coerce NA in columns of... |
| dup | Find duplications and pyrgos |
| duped | duped |
| duplicated.matrix | R-3.5.1 version of duplicated.matrix |
| enframe_list | data table-ize list elements and add name column |
| equals.gGraph | equals.gGraph |
| events | Events calling |
| events.to.gr | Events to GRanges |
| fitcn | fitcn |
| fusions | find fusions |
| gdist | gdist |
| gEdge | gEdge |
| gEdge.in | subset gEdge on overlaps |
| gEdge.over | gEdge over |
| gG | create gGraph |
| gGnome | gGnome |
| gGnome.js | Generate a gGnome.js instance |
| gGraph | gGraph |
| gGraph-constructor | simplify |
| gGraph.subset | subset gGraph on overlaps |
| gNode | gNode |
| gNode.loose | gNode.loose |
| gNode-over | subset gNode on overlaps |
| gNode-subset | subset gNode on overlaps |
| grapes-K-grapes | similar to setkey except a general use utility slower version... |
| gr.noval | get rid of mcols on GRanges/GRangesLists |
| gr.spreduce | reduce based on a field(s) to split by in elementMetadata of... |
| gW | create gWalk |
| gWalk | gWalk |
| gWalk.over | subset gWalk on overlaps |
| gWalk.subset | sets metadata of gWalk object (accessible through $dt... |
| haplograph | haplograph |
| initialize | copy |
| internal | Rcplex2 |
| intersect.gEdge | intersect.gEdge |
| intersect.gNode | intersect.gNode |
| intersect.Junction | intersect.Junction |
| isNA | is.na but also tests for "NA" character |
| jJ | parse junctions from a variety of formats |
| Junction | Junction |
| Junction-class-constructor | set |
| Junction.over | Junction over |
| Junction.subset | subset gEdge on overlaps |
| karyotype | karyotype |
| label.runs | label.runs |
| length | length.gNode |
| lengths | lengths |
| loosefix | loosefix |
| match3 | similar to setkey except a general use utility very slow... |
| merge | merge for undefined number of Junction objects |
| merge.Junction | merge junctions by overlaps with padding Merges a set of... |
| merge.repl | merging data tables with collapsing columns with the same... |
| microhomology | get microhomology |
| na2false | replace logical vector with NA to FALSE |
| peel | peel |
| pgv | Generate a PGV instance |
| phased.binstats | phased.binstats |
| ploidy | ploidy Computes ploidy i.e. average CN for a gGraph |
| proximity | Proximity analysis of two genomic regions and rearrangment... |
| ra.duplicated | ra.duplicated |
| ra.merge | Merges rearrangements represented by 'GRangesList' objects |
| rand.string | make a random string |
| read_cmap | read_cmap |
| read.juncs | read.juncs |
| read_xmap | read_xmap |
| reciprocal | Get reciprical connected junctions |
| refresh | refresh |
| rel2abs | rel2abs |
| rep_len2 | recycle vector along length OR nrow of object |
| rleseq | numbers up within repeating elements of a vector |
| rowMaxs | rowMaxs hack |
| rowMins | rowMins hack |
| run_gurobi | run_gurobi |
| seq_along2 | seq along either row of table or length of vector |
| seqinfo | seqinfo |
| seqlengths | seqlengths |
| seqlevels | seqlevels |
| setcols | convenience function to set columns sets columns of an object |
| setdiff | setdiff.gNode |
| setxor | setxor |
| simple | Simple Event Calling |
| sparse_subset | sparse_subset |
| split.gGraph | split.gGraph |
| spmelt | spMelt |
| sub-.gEdge | gEdge |
| sub-.gNode | gNode |
| sub-.gWalk | gWalk |
| sub-.Junction | Junction |
| sum.gGraph | sum.gGraph |
| tic | Find templated insertion chains (tics) |
| transplant | transplant donor subggraph into recipient |
| union | union.gNode |
| unique | unique.Junction |
| vaggregate | 'stats::aggregate', but returns vector |
| width | width |
