Files in cancer-genomics/trellis

Somatic structural variant analysis

R/AllGenerics.R R/Amplicon-class.R R/DNAcopy-class.R R/Deletion-class.R R/DeletionList-class.R R/DeletionParam-class.R R/ExonSubset-class.R R/GAlignmentPairs-utils.R R/GRanges-utils.R R/Preprocess-class.R R/Rearrangement-class.R R/RearrangementList-class.R R/RearrangementParams-class.R R/RearrangmentParams-class.R R/SegmentParam-class.R R/Transcripts-class.R R/acf.R R/alignment-utils.R R/amplicon-utils.R R/baf-utils.R R/blat-utils.R R/copynumber-methods.R R/data-utils.R R/data.R R/deletion-utils.R R/fasta-utils.R R/functions.R R/functions_for_CRAM.R R/fusion-utils.R R/galignment-utils.R R/germlineOutliers.R R/help.R R/improper-methods.R R/listCNVs.R R/listGenomeFilters.R R/preprocess-utils.R R/read_pairs.R R/rear_reads.R R/rearlist-utils.R R/rearrangement-utils.R R/recurrent.R R/segment.R R/seqinfo-utils.R R/uniprot.R contributing.md data-derived/axis_limits.R data-raw/amplicon_graph.R data-raw/bamviews.R data-raw/cgov44t_deletions.R data-raw/cgov44t_segments.R data-raw/complex_rearrangement.R data-raw/deletion.R data-raw/functions.R data-raw/ikzf2.R data-raw/rear_list.R data-raw/rearlist.R data-raw/rearrangements_cgov44t.R data-raw/rlist_with_invalid_split_reads.R data-raw/segmentation.R data-raw/sequence_tags.R data-raw/split_reads_cgov44t.R data-raw/split_reads_cgov7t.R data-raw/unmapped_blat_oralcleft.R data-raw/yap1-mamml_rear.R man/AmpliconGraph-class.Rd man/AmpliconGraph-constructor.Rd man/ClippedTranscripts-class.Rd man/DNAcopy-methods.Rd man/DeletionList-methods.Rd man/DeletionParam-class.Rd man/ExonSubset-class.Rd man/GAlignmentPairs.Rd man/PreprocessViews2-class.Rd man/PreprocessViews2-coercion.Rd man/Rearrangement-class.Rd man/RearrangementList-class.Rd man/RearrangementParams-class.Rd man/SegmentParam-class.Rd man/StructuralVariant-class.Rd man/Transcripts-class.Rd man/TranscriptsFusion-class.Rd man/aa_granges.Rd man/aberrantSep.Rd man/acf2.Rd man/add.info.Rd man/addFocalDupsFlankingAmplicon.Rd man/alignment-flags.Rd man/ampliconParams.Rd man/amplicon_graph.Rd man/amplicons-data.Rd man/annotateBlatRecords.Rd man/annotateRecurrent.Rd man/assays-PreprocessViews2-method.Rd man/binFragments.Rd man/binGCCorrect.Rd man/binMedians.Rd man/binNormalize.Rd man/binnedCounts.Rd man/blatScores.Rd man/blat_unmapped.Rd man/calls-method.Rd man/cbs2granges.Rd man/chromosome-methods.Rd man/clip.Rd man/codingJunctions.Rd man/copynumber-methods.Rd man/countParam.Rd man/countReads2.Rd man/deletion.Rd man/deletion_call.Rd man/deletions.Rd man/deletions2.Rd man/dt2ga2.Rd man/duplicatedGAlignmentPairs.Rd man/expandGRanges.Rd man/fasta.Rd man/fasta_unmapped.Rd man/filterBy-methods.Rd man/filterGermlineRear.Rd man/filterGermlineRearList.Rd man/filterPairedReads.Rd man/filterRear.Rd man/filterRearExperiment.Rd man/filterRearrangementList.Rd man/findCandidates2.Rd man/fiveTo3List.Rd man/fiveTo3Prime.Rd man/focalAmpliconDupRanges.Rd man/fractionLinkingTags.Rd man/fullTranscripts.Rd man/fuse-methods.Rd man/fuseCDS_Rlist.Rd man/fusionList.Rd man/fusionTable.Rd man/fusionTable2.Rd man/ga2gr.Rd man/germlineFilters.Rd man/germlineOutliers.Rd man/getCDS.Rd man/getImproperAlignmentPairs.Rd man/getProperAlignmentPairs.Rd man/getSequenceOfReads-methods.Rd man/getSequenceOfReads_bedops.Rd man/get_improper_readpairs.Rd man/get_readpairs.Rd man/get_readpairs2.Rd man/ggRearrange.Rd man/granges_copynumber.Rd man/groupAmplicons.Rd man/groupedVariant-method.Rd man/improper-methods.Rd man/inFrameFusions.Rd man/inFrameList.Rd man/inFrameNoStop.Rd man/indexRanges-method.Rd man/indexing-methods.Rd man/intOverWidth.Rd man/intersectionAligned.Rd man/isComplex.Rd man/isDuplicate.Rd man/isNotGermline.Rd man/is_valid_splits.Rd man/joinNearGRanges.Rd man/linkedBins-methods.Rd man/linkedTo.Rd man/listCNVs.Rd man/listDeletions.Rd man/listFusionData.Rd man/listGenomeFilters.Rd man/loadTx.Rd man/loadTxDb.Rd man/loadTxdbTranscripts.Rd man/makeAGraph.Rd man/modalRearrangement.Rd man/noPrematureStop.Rd man/numberImproper.Rd man/numberLinkingRP-methods.Rd man/numberOverlappingDeletions.Rd man/organizeReads.Rd man/organizeReferenceByFrame.Rd man/partitionAASequence.Rd man/paths.Rd man/pdata.Rd man/percentRearrangement.Rd man/preprocessData.Rd man/promoterCDS.Rd man/proper-methods.Rd man/properReadPairs.Rd man/properReadPairs_bedops.Rd man/properReadPairs_bedops2.Rd man/prp_makeRthinned.Rd man/rFilters.Rd man/rdsId.Rd man/readBlat.Rd man/readPairsAsSegments.Rd man/readPairsNearVariant.Rd man/rearDataFrame.Rd man/rearDataFrameList.Rd man/rear_cds-data.Rd man/rear_cgov7t.Rd man/rear_list-data.Rd man/rearrangedReadList.Rd man/rearrangedReads.Rd man/rearrangementData.Rd man/rearrangementType.Rd man/rearrangement_list.Rd man/recurrentDeletions.Rd man/recurrentDrivers.Rd man/reduceGenomeFilters.Rd man/referenceProtein.Rd man/removeAmbiguousAln.Rd man/rpSupportedDeletions.Rd man/sapply-methods.Rd man/scale_x_mb.Rd man/segmentBins.Rd man/segmentExperiment.Rd man/segments.Rd man/seqJunctionNearTx.Rd man/seqJunctionsInferredByPairedTags2.Rd man/seqJunctions_Rlist.Rd man/setScale-method.Rd man/sortByRead1.Rd man/splitReads.Rd man/svAF.Rd man/sv_amp_makeQuery.Rd man/sv_amplicon_exp.Rd man/sv_amplicons.Rd man/sv_amplicons2.Rd man/sv_amplicons2_bedops.Rd man/sv_amplicons2_bedops2.Rd man/sv_del_makeQuery.Rd man/sv_deletions.Rd man/sv_deletions_bedops.Rd man/sv_deletions_bedops2.Rd man/tag_sequenceExperiment.Rd man/tags-methods.Rd man/thinProperPairs.Rd man/thinReadPairs.Rd man/threshold.Rd man/totalWidth.Rd man/transcript-accessors.Rd man/translateCDS.Rd man/trellis.Rd man/tumorProtein.Rd man/type_rearrangement.Rd man/uncouple.Rd man/uniprotFeatures.Rd man/unmapped_read.Rd man/unmapped_read_bedops.Rd man/validFusions.Rd man/variant-methods.Rd tests/testthat.R tests/testthat/deletion-4500T3.R tests/testthat/test_AmpliconGraph.R tests/testthat/test_CNAObject.R tests/testthat/test_DeletionList.R tests/testthat/test_DeletionParam.R tests/testthat/test_ExonSubset.R tests/testthat/test_Rearrangement.R tests/testthat/test_RearrangementList.R tests/testthat/test_RearrangementParams.R tests/testthat/test_StructuralVariant.R tests/testthat/test_Transcript.R tests/testthat/test_addFocalDupsFlankingAmplicon.R tests/testthat/test_amplicon_regressions.R tests/testthat/test_annotation.R tests/testthat/test_axis_limits.R tests/testthat/test_barcodes.R tests/testthat/test_binCounts.R tests/testthat/test_binFragments.R tests/testthat/test_binGCCorrect.R tests/testthat/test_binNormalize.R tests/testthat/test_blatScores.R tests/testthat/test_candidate_regressions.R tests/testthat/test_chromosome.R tests/testthat/test_complex_rearrangement.R tests/testthat/test_deletion_regressions.R tests/testthat/test_duplicatedGAlignmentPairs.R tests/testthat/test_expandGRanges.R tests/testthat/test_filter_regressions.R tests/testthat/test_fiveTo3prime.R tests/testthat/test_focalAmpDupRanges.R tests/testthat/test_fusionTable2.R tests/testthat/test_fusion_regression.R tests/testthat/test_genomeFilters.R tests/testthat/test_getImproperAlignmentPairs.R tests/testthat/test_getSequenceOfReads.R tests/testthat/test_ggRearrange.R tests/testthat/test_ikzf2.R tests/testthat/test_improperAlignmentParams.R tests/testthat/test_inframe.R tests/testthat/test_intOverWidth.R tests/testthat/test_invalid_split_reads.R tests/testthat/test_joinNeargRanges.R tests/testthat/test_linkDuplicatedRanges.R tests/testthat/test_organizeReads.R tests/testthat/test_ovarian_cellLines.R tests/testthat/test_overlappingHemizygous.R tests/testthat/test_promoter.R tests/testthat/test_properReadPairs.R tests/testthat/test_protein_domains.R tests/testthat/test_rearrangedReads.R tests/testthat/test_recurrentDeletions.R tests/testthat/test_reviseEachJunction.R tests/testthat/test_segmentation.R tests/testthat/test_seqinfo.R tests/testthat/test_split_reads.R tests/testthat/test_vaf.R tests/testthat/test_vignette_deletion.R tests/testthat/test_writeImproperAlignments.R tests/testthat/test_writeToFasta.R vignettes/trellis.Rmd