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.

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