Man pages for mskilab/gUtils
R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

anchorliftanchorlift
dt2grConvert data.table to GRanges
example_dnaseDNAaseI hypersensitivity sites for hg19A
example_genesRefSeq genes for hg19
gr2dtConverts 'GRanges' to 'data.table'
grbindConcatenate 'GRanges', robust to different 'mcols'
gr.breaksBreak GRanges at given breakpoints into disjoint gr
gr.chrPrepend "chr" to 'GRanges seqlevels'
gr.collapseCollapse adjacent ranges
gr.covgr.cov
gr.diceDice up 'GRanges' into 'width = 1' 'GRanges' spanning the...
gr.disjoinGenomicRanges disjoin with some spice Identical to GRanges...
gr.distPairwise distance between two 'GRanges'
gr.duplicatedAllows to restrict duplicates using "by" columns and allows...
gr.endGet the right ends of a 'GRanges'
gr.findoverlapsWrapper to 'GenomicRanges::findOverlaps' with added...
gr.fix"Fixes" 'seqlengths' / 'seqlevels'
gr.flattenLay ranges end-to-end onto a derivate "chromosome"
gr.flipstrandFlip strand on 'GRanges'
grfoMetadata join with coordinates as keys (wrapper to...
grfo-shortcutgr.findoverlaps (respects strand)
gr.inVersatile implementation of 'GenomicRanges::over'
gr.in-shortcutsubset x on y ranges wise ignoring strand
gr.in-strand-shortcutSubset x on y ranges wise respecting strand
grl1Fake rearrangement data (set 1)
grl2Fake rearrangement data (set 2)
grlbindConcatenate 'GRangesList' objects.
grl.evalevaluate and aggregate expression on GRanges column in...
grl.hiCHiC data for chr14 from Lieberman-Aiden 2009 (in hg19),...
grl.inCheck intersection of 'GRangesList' with windows on genome
grl.pivotPivot a 'GRangesList', inverting "x" and "y"
grl.reducegrl.reduce
grl.stringCreate string representation of 'GRangesList'
grl.stripnamesRemove 'GRanges' names inside a 'GRangesList'
grl.unlistRobust unlisting of 'GRangesList' that keeps track of origin
gr.matchAlternative 'GenomicRanges::match' that accepts additional...
gr.mergemerge GRanges using coordinates as primary key
gr.midGet the midpoints of 'GRanges' ranges
gr.nochrRemove chr prefix from GRanges seqlevels
gr.nudgeShift GRanges left
gr.nudge-shortcutNudge GRanges right
gr.pairflipCreate pairs of ranges and their strand-inverse
gr.queryquery ranges by applying an expression to ranges metadata
gr.randGenerate random 'GRanges' on genome
gr.sampleRandomly sample 'GRanges' intervals within territory
gr.setdiff'BiocGenerics::setdiff' shortcut (strand agnostic)
gr.simplifySimplify granges by collapsing all non-overlapping adjacent...
gr.startGet GRanges corresponding to beginning of range
gr.stringReturn UCSC style interval string corresponding to 'GRanges'...
gr.stripstrandgr.stripstrand
gr.subApply 'gsub' to seqlevels of a 'GRanges'
gr.tileTile ranges across 'GRanges'
gr.tile.mapgr.tile.map
gr.trimTrims pile of 'GRanges' relative to the specified <local>...
gr.valAnnotate 'GRanges' with values from another 'GRanges'
gr.val-fractionalgr.val shortcut to get fractional overlap of gr1 by gr2,...
gr.val-meangr.val shortcut to get mean values of subject "x" meta data...
gr.val-numbersgr.val shortcut to get total numbers of intervals in gr2...
gr.val-Ogr.val shortcut to get fractional overlap of gr1 by gr2,...
gr.val-shortcutgr.val shortcut to get total numbers of intervals in gr2...
gr.val-strandgr.val shortcut to total per interval width of overlap of gr1...
gr.val-totalgr.val shortcut to total per interval width of overlap of gr1...
hg_seqlengthsOutput standard human genome seqlengths
parse.grparse.gr
parse.grlparse.grl
ra.dedupDeduplicates rearrangements represented by 'GRangesList'...
ra.duplicatedShow if junctions are Deduplicated
ra.mergeMerges rearrangements represented by 'GRangesList' objects
ra.overlapsra.overlaps
rle.queryQueries an 'RleList' representing genomic data
rrbindImproved 'rbind' for intersecting/union columns of...
seg2grConvert GRange like data.frames into GRanges
si'Seqinfo' object for hg19
si2grCreate 'GRanges' from 'Seqinfo' or 'BSgenome'
streduceReduce 'GRanges' and 'GRangesList' to miminal footprint
mskilab/gUtils documentation built on Nov. 22, 2017, 9:38 p.m.