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

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.chrPrepend "chr" to 'GRanges seqlevels'
gr.collapseCollapse adjacent ranges
gr.diceDice up 'GRanges' into 'width = 1' 'GRanges' spanning the...
gr.disjoinGenomicRanges disjoin with some additional functionality
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-shortcutshortcut for gr.findoverlaps (strand-specific)
gr.inVersatile implementation of 'GenomicRanges::findOverlaps' x on y ranges while ignoring strand (strand-agnostic) x on y ranges, strand-specific
grl1Fake rearrangement data (set 1)
grl2Fake rearrangement data (set 2)
grl.bindConcatenate '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.stringCreate string representation of 'GRangesList'
grl.unlistRobust unlisting of 'GRangesList' that keeps track of origin
gr.matchAlternative 'GenomicRanges::match' that accepts additional...
gr.mergemerge GRanges by 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.simplifyCalculates pairwise distance for rearrangements represented...
gr.startGet GRanges corresponding to beginning of range
gr.stringReturn UCSC style interval string corresponding to 'GRanges'...
gr.subApply 'gsub' to seqlevels of a 'GRanges'
gr.tileTile ranges across 'GRanges'
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
rle.queryQueries an 'RleList' representing genomic data
rrbindImproved 'rbind' for intersecting/union columns of...
seg2grConvert GRanges-like data.frame into GRanges
si'Seqinfo' object for hg19
si2grCreate 'GRanges' from 'Seqinfo' or 'BSgenome'
standardize_segsTakes and returns segs data frame standardized to a single...
streduceReduce 'GRanges' and 'GRangesList' to miminal footprint
mskilab/gUtils documentation built on Feb. 18, 2018, 11:53 a.m.