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| .adjustRelativeInsLocs | Helper functions for selectAlnRegions |
| .checkRelativeLocs | Helper functions for selectAlnRegions |
| .explodeCigarOpCombs | .explodeCigarOpCombs |
| .findMismatches | formatVarLabels |
| .formatVarLabels | formatVarLabels |
| .getAxisCoords | .getAxisCoords |
| .intersperse | .intersperse |
| .invertKeepRanges | Helper functions for selectAlnRegions |
| .offsetIndices | Helper functions for selectAlnRegions |
| abifToFastq | Read a file in ab1 (Sanger) format and convert to fastq |
| addClipped | Extrapolates mapping location from clipped, aligned reads |
| addClipped-method | Extrapolates mapping location from clipped, aligned reads |
| addCodonFrame | Internal CrispRVariants function for indicating codon frame on an alignment tile plot |
| alleles | Get allele names |
| alleles-method | Get allele names |
| alns | Get alignments |
| alns-method | Get alignments |
| annotateGenePlot | Plots and annotates transcripts |
| arrangePlots | Arrange plots for plotVariants:CrisprSet |
| barplotAlleleFreqs | Plots barplots of the spectrum of variants for a sample set |
| barplotAlleleFreqs-method | Plots barplots of the spectrum of variants for a sample set |
| collapsePairs | Internal CrispRVariants function for collapsing pairs with concordant indels |
| consensusSeqs | Get consensus sequences for variant alleles |
| consensusSeqs-method | Get consensus sequences for variant alleles |
| countDeletions | Count the number of reads containing an insertion or deletion |
| countDeletions-method | Count the number of reads containing an insertion or deletion |
| countIndels | Count the number of reads containing an insertion or deletion |
| countIndels-method | Count the number of reads containing an insertion or deletion |
| countInsertions | Count the number of reads containing an insertion or deletion |
| countInsertions-method | Count the number of reads containing an insertion or deletion |
| CrisprRun | CrisprRun class |
| CrisprRun-class | CrisprRun class |
| CrisprSet | CrisprSet class |
| CrisprSet-class | CrisprSet class |
| dispatchDots | dispatchDots |
| excludeFromBam | Removes reads from a bam file |
| findChimeras | Find chimeric reads |
| findSNVs | Find frequent SNVs |
| findSNVs-method | Find frequent SNVs |
| getChimeras | Get chimeric alignments |
| getChimeras-method | Get chimeric alignments |
| getInsertionsTable | getInsertionsTable |
| gol | Variant sequences from golden clutch 1 (Burger et al) |
| gol_clutch1 | Variant sequences from golden clutch 1 (Burger et al) |
| indelLabels | indelLabels |
| indelPercent | Count the number of reads containing an insertion or deletion |
| indelPercent-method | Count the number of reads containing an insertion or deletion |
| makeAlignmentTilePlot | Internal CrispRVariants function for creating the plotAlignments background |
| mergeChimeras | mergeChimeras |
| mergeCrisprSets | Merge two CrisprSets |
| mergeCrisprSets-method | Merge two CrisprSets |
| mismatchLabels | nonindelLabels |
| mutationEfficiency | Get mutation efficiency |
| mutationEfficiency-method | Get mutation efficiency |
| narrowAlignments | Narrow a set of aligned reads to a target region |
| narrowAlignments-method | Narrow a set of aligned reads to a target region |
| plotAlignments | Plot alignments with respect to a reference sequence |
| plotAlignments-method | Plot alignments with respect to a reference sequence |
| plotChimeras | Display a dot plot of chimeric alignments |
| plotFreqHeatmap | Plot a table of counts with colours indicating frequency |
| plotFreqHeatmap-method | Plot a table of counts with colours indicating frequency |
| plotVariants | Plot alignments, frequencies and location of target sequence |
| plotVariants-method | Plot alignments, frequencies and location of target sequence |
| rcAlns | Internal CrispRVariants function for determining read orientation |
| readsByPCRPrimer | Finds overlaps between aligned reads and PCR primers |
| readsByPCRPrimer-method | Finds overlaps between aligned reads and PCR primers |
| readsToTarget | Trims reads to a target region. |
| readsToTarget-method | Trims reads to a target region. |
| readsToTargets | Trims reads to a target region. |
| readsToTargets-method | Trims reads to a target region. |
| readTargetBam | Internal CrispRVariants function for reading and filtering a bam file |
| refFromAlns | refFromAlns |
| refFromAlns-method | refFromAlns |
| reverseCigar | Reverses the order of operations in a cigar string |
| rmMultiPCRChimera | Remove chimeric reads overlapping multiple primers |
| rmMultiPCRChimera-method | Remove chimeric reads overlapping multiple primers |
| selectAlnRegions | Creates a text alignment from a set of cigar strings |
| selectOps | selectOps |
| selectOps-method | selectOps |
| seqsToAln | Creates a text alignment from a set of cigar strings |
| setDNATileColours | Sets colours for plotting aligned DNA sequences. |
| setMismatchTileColours | Sets colours for plotting mismatches in aligned DNA sequences. |
| transformAlnsToLong | Transform data for plotting |
| variantCounts | Get variant counts |
| variantCounts-method | Get variant counts |
| writeFastq | Append a sequence to a fastq file |