Man pages for cancer-genomics/trellis
Somatic structural variant analysis
| aa_granges | Convert tumor amino acid ranges to a GRanges object |
| aberrantSep | Assesses whether two reads in a pair are aberrantly separated... |
| acf2 | Compute the autocorrelation at a specific lag |
| addFocalDupsFlankingAmplicon | Add focal amplicons that flank an amplicon seed |
| add.info | Add seqinfo to dataframe (for CRAM) |
| alignment-flags | Creates a default set of flags for reading improperly paired... |
| amplicon_graph | An AmpliconGraph object |
| AmpliconGraph-class | A class for representing somatic amplicons |
| AmpliconGraph-constructor | Constructor for AmpliconGraph |
| ampliconParams | Lists germline filters and parameters for filtering amplicons |
| amplicons-data | An example AmpliconGraph |
| annotateBlatRecords | Annotate blat records |
| annotateRecurrent | Annotate table of amplified genes with linked drivers and the... |
| assays-PreprocessViews2-method | Accessor for reading assay data saved to disk |
| binFragments | Counts the number of read fragments mapped to bins |
| binGCCorrect | Correct coverage for GC content |
| binMedians | Computes a median normalized coverage across samples for each... |
| binnedCounts | Counts reads mapped to genomic intervals |
| binNormalize | Normalize counts |
| blatScores | blatScores assesses whether the improper read pairs at a... |
| blat_unmapped | BLAT alignment of reads that were unmapped by ELAND |
| calls-method | Type of deletion |
| cbs2granges | Coerce a DNAcopy object to GRanges |
| chromosome-methods | Extract autosomal (human) sequence levels |
| clip | Select CDS involved in a fusion |
| ClippedTranscripts-class | A container for clipped transcripts |
| codingJunctions | Select sequence junctions in which both the five-prime and... |
| copynumber-methods | Accessor for 'copy' assays |
| countParam | Generate parameters that specify which reads in a bam file to... |
| countReads2 | Count reads in bamRanges of a BamViews object |
| deletion | A StructuralVariant object |
| deletion_call | Creates a StructuralVariant object, linking genomic intervals... |
| DeletionList-methods | GRangesList-derived class for deletions |
| DeletionParam-class | Parameter class for calling deletions |
| deletions | A deletions object of class StructuralVariant |
| deletions2 | A StructuralVariant object |
| DNAcopy-methods | Class for storing circular binary segmentation results |
| dt2ga2 | Convert dataframe to GAlignment (for CRAM) |
| duplicatedGAlignmentPairs | Determines which rows from a 'GAlignmentPairs' object are... |
| ExonSubset-class | Container for storing information to subset transcripts |
| expandGRanges | Expand a genomic interval |
| fasta | Helper function to write tags to FASTA files |
| fasta_unmapped | Write the read sequences of unmapped-mapped read pairs to... |
| filterBy-methods | Remove the genomic intervals in query that overlap with... |
| filterGermlineRear | Applies germline CNV and sequence-based filters for... |
| filterGermlineRearList | Exclude linked tag cluster that overlap with germline CNVs or... |
| filterPairedReads | Remove duplicates paired r |
| filterRear | Filter candidate rearrangements for germline |
| filterRearExperiment | Exclude linked tag cluster that overlap with germline CNVs or... |
| filterRearrangementList | Applies several filters for somatic rearrangements |
| findCandidates2 | Finds candidate somatic rearrangements |
| fiveTo3List | Reorders each rearrangement as two 5-prime to 3-prime... |
| fiveTo3Prime | Put the linked genomic intervals in 5-prime to 3-prime order... |
| focalAmpliconDupRanges | Identify lower copy focal amplicons (possibly duplicatons)... |
| fractionLinkingTags | The fraction of improper read pairs that link two clusters of... |
| fullTranscripts | List full transcripts for genes spanning a rearrangement |
| fuseCDS_Rlist | Extract the CDS involved in each rearrangement of a... |
| fuse-methods | Fuse transcripts |
| fusionList | A title |
| fusionTable | Determine all possible fusions of a Rearrangement object |
| fusionTable2 | Create a table of in-frame fusions |
| ga2gr | Convert GAlignmentPairs to GRanges while maintaining read... |
| GAlignmentPairs | Constructor for an empty GAlignmentPairs object |
| germlineFilters | Identify focal, somatic hemizygous deletions and somatic... |
| germlineOutliers | Identify genomic regions with outlier preprocess read depth... |
| getCDS | Finds all genes overlapping a rearrangement (ignoring strand)... |
| getImproperAlignmentPairs | Extract all improperly paired reads from a bam file as a... |
| get_improper_readpairs | Extract all improperly paired reads from an object with... |
| getProperAlignmentPairs | Extract properly paired reads from a bam file |
| get_readpairs | Parse BAM file for improper read pairs near a set of GRanges |
| get_readpairs2 | Extract reads from a bam file |
| getSequenceOfReads_bedops | getSequenceOfReads for CRAM |
| getSequenceOfReads-methods | Extract sequences of reads supporting rearrangements from a... |
| ggRearrange | ggplot wrapper for plotting reads supporting a rearrangement |
| granges_copynumber | Compute the mean normalized read-depth for a set of intervals |
| groupAmplicons | Assign a group id for nodes that are linked |
| groupedVariant-method | Accessor for variable indicating a grouping for deletions |
| improper-methods | Accessor for improper read pairs |
| indexing-methods | Accessor of an index for the proper read pairs |
| indexRanges-method | Indexes the GRanges of a BamViews-derived class |
| inFrameFusions | Evaluates whether a rearranged DNA sequence is in-frame |
| inFrameList | Evaluate whether fusion amino acid sequence is a subsequence... |
| inFrameNoStop | Combine the in-frame and no-premature-stop LogicalLists |
| intersectionAligned | Compute the intersection of the split read alignment |
| intOverWidth | Find the fraction of genomic interval overlapping with... |
| isComplex | Ad-hoc assessment of the complexity of a rearrangement using... |
| isDuplicate | Assesses whether any read pairs are duplicates in a... |
| isNotGermline | Assess whether a region can be attributable to a germline CNV... |
| is_valid_splits | Check that the split reads available for each rearrangement... |
| joinNearGRanges | Merge adjacent amplicons that have a similar segment mean |
| linkedBins-methods | Accessor for clusters of reads belonging to improper read... |
| linkedTo | A region linked by improperly paired reads |
| listCNVs | List amplicons and deletions identified for a single sample |
| listDeletions | Extract a GRangesList of all identified deletions in a... |
| listFusionData | Collect fusion-related data into a single list |
| listGenomeFilters | Genomic filters for the somatic amplicon analysis |
| loadTx | Load Txdb object |
| loadTxDb | Loads TxDb object from TxDb.Hsapiens.UCSC.<build>.refGene |
| loadTxdbTranscripts | Load transcripts, CDS, and a txdb object for a user-specified... |
| makeAGraph | Initialize a graph object for amplicon analyses |
| modalRearrangement | Accessor for the modal rearrangement of a linked tag cluster |
| noPrematureStop | Assess whether there are any premature stop codons |
| numberImproper | Extract number of improper reads for each element in a... |
| numberLinkingRP-methods | Calculate the number of read pairs that link two clusters of... |
| numberOverlappingDeletions | Tabulate the frequency a gene has a deletion |
| organizeReads | Organize improper read pairs supporting a rearrangement into... |
| organizeReferenceByFrame | Organize reference amino acid sequences by frame |
| partitionAASequence | Partition the amino acid sequence of the fusion protein into... |
| paths | Accessor for file paths |
| pdata | A list of preprocess data for calling deletion/amplification |
| percentRearrangement | The fraction of improper read pairs supporting the modal... |
| preprocessData | Create a list of relevant information for calling... |
| PreprocessViews2-class | A container for storing views of preprocessed data |
| PreprocessViews2-coercion | Coerce a 'PreprocessViews2' object to a... |
| promoterCDS | Create the full CDS of transcripts for those in which only... |
| proper-methods | Get / set properly paired reads |
| properReadPairs | Import properly paired reads from a bam file |
| properReadPairs_bedops | Proper read pairs near variant (properReadPairs for CRAM) |
| properReadPairs_bedops2 | Second part of properReadPairs_bedops |
| prp_makeRthinned | First part of properReadPairs_bedops |
| rdsId | Helper for creating filenames with .rds extension |
| readBlat | Read output from the command-line blat |
| readPairsAsSegments | Represent read pairs as segments |
| readPairsNearVariant | Extract all mapped read pairs near a deletion(s) |
| rear_cds-data | An example Transcripts object |
| rear_cgov7t | A RearrangementList from ovarian cell line CGOV7T |
| rearDataFrame | Create a data.frame of rearranged read pairs and split reads... |
| rearDataFrameList | Creates a data.frame with both possible 5 to 3 prime... |
| rear_list-data | An example RearrangementList |
| rearrangedReadList | Identify rearranged reads - initiallly unmapped reads that... |
| rearrangedReads | Identify rearranged reads - initiallly unmapped reads that... |
| Rearrangement-class | A class for storing rearrangement data |
| rearrangementData | Creates a list object of data required to identify... |
| rearrangement_list | An example RearrangementList object |
| RearrangementList-class | Constructor for 'RearrangementList' class |
| RearrangementParams-class | Parameter class for rearrangement analysis |
| rearrangementType | Determine the type of rearrangement supported by each... |
| recurrentDeletions | Aggregate deletions to the gene-level when evaluating... |
| recurrentDrivers | Table of recurrent drivers |
| reduceGenomeFilters | Create a reduced set of germline and sequence filters |
| referenceProtein | Translate the unrearranged (reference) sequence |
| removeAmbiguousAln | Removes rearrangements for which the BLAT-aligned reads do... |
| rFilters | Construct list of filters for somatic rearrangement analyses |
| rpSupportedDeletions | Counts the number of improper read pairs supporting a... |
| sapply-methods | Functionals for structural variant classes |
| scale_x_mb | Use MB scale in gg-style plots |
| segmentBins | Segment log2-transformed and GC-adjusted counts using... |
| segmentExperiment | Segments log2-transformed and GC-adjusted counts. |
| SegmentParam-class | A class for storing segmentation parameters |
| segments | A GRanges object of segmentation data |
| seqJunctionNearTx | Evaluates whether sequence junction of a rearrangement is... |
| seqJunctionsInferredByPairedTags2 | Constructs a Rearrangement object of unlinked tag-clusters |
| seqJunctions_Rlist | Use split reads for each rearrangement to more precisely... |
| setScale-method | Set numeric scale for 'PreprocessViews2' object |
| sortByRead1 | Sort GRanges object with read pairs R1 and R2 by start of R1 |
| splitReads | Accessor for split read alignments |
| StructuralVariant-class | The StructuralVariant class stores data pertaining to somatic... |
| svAF | Compute allele frequencies at germline heterozygous positions... |
| sv_amplicon_exp | Identify somatic amplicons and grouped amplicons |
| sv_amplicons | Construct an AmpliconGraph from a BamViews object |
| sv_amplicons2 | Construct an AmpliconGraph from a BamViews object |
| sv_amplicons2_bedops | sv_amplicons2 for CRAM |
| sv_amplicons2_bedops2 | Second part of sv_amplicons2_bedops |
| sv_amp_makeQuery | First part of sv_amplicons2_bedops |
| sv_deletions | Creates a StructuralVariant object |
| sv_deletions_bedops | Define new functions for sv_deletions (for CRAM) |
| sv_deletions_bedops2 | Second part of sv_deletions_bedops |
| sv_del_makeQuery | First part of sv_deletions_bedops |
| tag_sequenceExperiment | Extracts read sequences |
| tags-methods | Accessor for all the improper reads |
| thinProperPairs | Thin proper read pairs to reduce overplotting |
| thinReadPairs | Extract read pairs from a 'StructuralVariant' object |
| threshold | Threshold values of a numeric vector |
| totalWidth | Find total width of a 'GRanges' object |
| transcript-accessors | Accessor for transcript from Transcripts-derived class |
| Transcripts-class | Container for storing CDS near a sequence junction |
| TranscriptsFusion-class | A container for fused transcripts |
| translateCDS | Translate the CDS in each of the three possible reading... |
| trellis | Somatic structural variant analysis |
| tumorProtein | Translate the sequence of a rearranged DNA sequence |
| type_rearrangement | Summary stats for rearrangement object |
| uncouple | Uncouple linked bins |
| uniprotFeatures | Extract features from uniprot database |
| unmapped_read | Extract unmapped reads with a mapped mate from a bam file |
| unmapped_read_bedops | unmapped_read for CRAM |
| validFusions | Create a List of in-frame fusions with no premature stops |
| variant-methods | Extract deletion regions from a StructuralVariant object |
