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 | Accessor for the combination of strands involved in a... |
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 |
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