Files in GenomicInteractions

Utilities for handling genomic interaction data

README.md R/annotators.R R/viewPoints.R R/getters.R R/DocumentData.R R/InteractionTrack-class.R R/export.R R/subsetting.R R/plotSummaryStats.R R/setters.R R/import.R R/GenomicInteractions-package.R R/summarise_annotations.r R/helpers.R R/export.igraph.R R/library.R R/calculateDistances.R R/processing.R R/GenomicInteractions-class.R vignettes/hic_vignette.Rmd vignettes/chiapet_vignette.rmd man/dot-importHicLib.Rd man/removeDups.Rd man/export.bedpe.Rd man/plotDists.Rd man/GenomicInteractions-package.Rd man/summariseByFeaturePairs.Rd man/summariseByFeatures.Rd man/countsBetweenAnchors-methods.Rd man/categoriseInteractions.Rd man/plotCisTrans.Rd man/plotInteractionAnnotations.Rd man/get_binom_ligation_threshold.Rd man/GInteractions-subsetByFeatures-methods.Rd man/plotSummaryStats.Rd man/dot-importHomer.Rd man/makeGenomicInteractionsFromFile.Rd man/annotateRegions.Rd man/thymus_enh.Rd man/dot-readBam.Rd man/resetAnnotations.Rd man/export.chiasig.Rd man/InteractionTrack.Rd man/plotCounts.Rd man/hic_example_data.Rd man/InteractionTrack-class.Rd man/mm9_refseq_promoters.Rd man/plotViewpoint.Rd man/export.igraph.Rd man/GenomicInteractions.Rd man/updateObject-GenomicInteractions-method.Rd man/calculateDistances.Rd man/dot-validateInput.Rd man/plotAvgViewpoint.Rd man/export.bed12.Rd man/dot-readTwoBams.Rd man/getters.Rd man/GenomicInteractions-class.Rd man/sameStrand.Rd man/viewPoint.Rd man/asBED-GInteractions-method.Rd man/hg19.refseq.transcripts.Rd man/dot-processChiapetName.Rd man/availableDisplayPars.Rd man/InteractionHelpers.Rd man/get_self_ligation_threshold.Rd man/sum-GInteractions-method.Rd man/annotateInteractions.Rd man/setters.Rd tests/testthat.R tests/testthat/test_viewpoint.R tests/testthat/test_annotation.R tests/testthat/test_getters.R tests/testthat/test_import.R tests/testthat/test_valid.R tests/testthat/test_summarystats.R inst/doc/chiapet_vignette.R inst/doc/hic_vignette.Rmd inst/doc/hic_vignette.R inst/doc/chiapet_vignette.rmd