Summarize, annotate and visualize genomic intervals with R/BioC package genomation
GenomicintervalsGenomicintervalsarethebasisofgenomeannota3on.Intervalscancontainsimplyloca3oninforma3on(TFBSloca3ons)orcancontainavarietyofscores,withdifferentscales,suchaspercentmethyla3on,ChIP-seqenrichmentorreadcoverage.
Windows/regionsofinterestoverthegenomeSummaryofgenomicintervalsoverdifferentsub-genomiccontextsorwindowsofinterestisthenecessaryfirststepinmakinginferenceaboutthebiologicalimportanceofthedata.Thecanbeofequallength(Ex:pre-definedregionsaroundTSS)ornot(Ex:exons,transcriptorCpGislands)
ExtractgenomicintervalsforwindowsofinterestGenomicintervalscouldbeextractedforwindowsofinterestandstoredinmatrixformat.Ifthewindowsarenotofequallength,thenbinningstrategiescanbeusedtocreateequalnumberofbinsoverthosewindowsands3lluseamatrixtostoreinforma3on.
VisualizethesummaryofgenomicintervalsThematricesthatdescribedabovecanbevisualizedusingheatmapsormeta-regionplots.Meta-regionplotsshowtheaveragevalueofthesignalfromgenomicintervalsoverthewindowsofinterest,thiscouldbealineplotoraheatmapwherecolorsindicateaveragevalues.Anothertypeheatmapcouldbeusedtoshowthevaluesformatricesthatcontainthesignalvalueforgenomicintervalsoverthewindows.Intheseheatmaps,everyrowrepresentsawindowandeverycolumnisabase-posi3onorabin.
ReadgenomicintervalsintoRGenomicintervalsofanykindcanberedintoRusingthefunc3onsbelow,allwhichreturnGRangesorGRangesListobjects:readGeneric(file,…)canreadgenerictextfileswithgenomicintervalinforma3on.readBed(file,...)canreadBEDfiles.readTranscriptFeatures(file,…) canreadBED12fileswithexon/intronstructure.gffToGRanges canreadaGFFfile. readBroadPeak,readNarrowPeak, readFeatureFlankareotherconveniencefunc3onstoreadBED-likefiles.
ExtractgenomicintervalsforwindowsofinterestinRGenomicintervalscouldbeextractedforwindowsofinterestusingScoreMatrix(target,windows) &ScoreMatrixBin(target,windows) func3ons.Thesefunc3onscanhandleBAM,BigWigfilesandGRangesobjectsasinputs.patternMatrix() returnstherela3veloca3onsorscoresofk-mersormo3fs,usefulforanalyzingChIP-seq.AllofthesereturnScoreMatrixorScoreMatrixListobjects.Theseobjectscanbemanipulatedfurtherusing orderBy, binMatrix, scaleScoreMatrix, scaleScoreMatrixList, intersectScoreMatrixList and [] func3ons.
VisualizethesummaryofgenomicintervalsinRheatMatrix(scoreMatrixobj) andmultiHeatMatrix(scoreMatrixListObj) makestheheatmapsforwindowsofinterest. plotMeta()makesmeta-regionplotsandheatMeta() makesmeta-regionheatmaps.Thesefunc3onsreturnvaluesinvisiblyseerespec3vehelppagesforfunc3ons.Intergenic
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meta-region plots meta-region heatmaps heatmaps for genomic interval sets
Piecharts for annotation
Annota3onforgenomicintervalsinRAnnota3onsummariesfortargetgenomicintervalscanbeobtainedbyannotateWithFeatures().Theresul3ngobjectcanbevisualizedbyplotTargetAnnotation() forpiechartandheatTargetAnnotation() foraheatmapofannota3onoverlappingpercentages.
Contributors:AltunaAkalin[aut,cre],VedranFranke[aut,cre],KatarzynaWreczycka[aut],AlexanderGosdschan[ctb],LizIng-Simmons[ctb]CitaCon:AkalinA,FrankeV,VlahovicekK,MasonCE,SchubelerD.(2015).Bioinforma3cs.Doi:10.1093/bioinforma3cs/btu775
Genomicintervalswithdifferentkindsofinforma3on
Extractsubsetofgenomicintervalsforwindowsofinterest
Meta-regionlineplots
Meta-regionheatmap
heatmapsforgenomicintervals
Annota3onpiecharts Annota3onheatmaps
Annota3onforgenomicintervalsGenomicintervalssuchasChIP-seqpeaksordifferen3allymethylatedregionsneedstobeannotatedfurtherwithknowngenomicannota3onssuchaspromoter,intron,exonstructuresofthegenes.Thisgivesaddi3onalinforma3onforfunc3onalcharacteriza3onofthegenomicintervals.Thisusuallyrepresentedaspercentofgenomicfeaturesoverlappingwiththeannota3on.
urls:hap://bioinforma3cs.mdc-berlin.de/genoma3onhap://www.biconductor.org/release/genoma3onInstallgenomaCon: OR
devtools::install_github(”BIMSBbioinfo/genomation”, build_vig=F)
source("https://bioconductor.org/biocLite.R") ; biocLite(“genomation”)
Visualizesummariesandannota3onforgenomicintervals
Misc.func3onsgetRandomEnrichment() calculatesthesignificanceofassocia3onbetweentwosetsofgenomicsintervals.
Validforpackageversion=>1.5.6