Man pages for HLindsay/CrispRVariants
Tools for counting and visualising mutations in a target location
| abifToFastq | Read a file in ab1 (Sanger) format and convert to fastq |
| addClipped | Extrapolates mapping location from clipped, aligned reads |
| addCodonFrame | Internal CrispRVariants function for indicating codon frame... |
| alleleLabelsHelpers | formatVarLabels |
| alleles | Get allele names |
| alns | 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 |
| collapsePairs | Internal CrispRVariants function for collapsing pairs with... |
| consensusSeqs | Get consensus sequences for variant alleles |
| CrisprRun-class | CrisprRun class |
| CrisprSet-class | CrisprSet class |
| dispatchDots | dispatchDots |
| excludeFromBam | Removes reads from a bam file |
| explodeCigarOpCombs | .explodeCigarOpCombs |
| findChimeras | Find chimeric reads |
| findSNVs | Find frequent SNVs |
| getAxisCoords | .getAxisCoords |
| getChimeras | Get chimeric alignments |
| getInsertionsTable | getInsertionsTable |
| gol_clutch1 | Variant sequences from golden clutch 1 (Burger et al) |
| indelCounts | Count the number of reads containing an insertion or deletion |
| indelLabels | indelLabels |
| intersperse | .intersperse |
| makeAlignmentTilePlot | Internal CrispRVariants function for creating the... |
| mergeChimeras | mergeChimeras |
| mergeCrisprSets | Merge two CrisprSets |
| mismatchLabels | nonindelLabels |
| mutationEfficiency | Get mutation efficiency |
| narrowAlignments | Narrow a set of aligned reads to a target region |
| plotAlignments | 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 |
| plotVariants | Plot alignments, frequencies and location of target sequence |
| rcAlns | Internal CrispRVariants function for determining read... |
| readsByPCRPrimer | Finds overlaps between aligned reads and PCR primers |
| readsToTarget | Trims reads to a target region. |
| readTargetBam | Internal CrispRVariants function for reading and filtering a... |
| refFromAlns | refFromAlns |
| reverseCigar | Reverses the order of operations in a cigar string |
| rmMultiPCRChimera | Remove chimeric reads overlapping multiple primers |
| selectAlnRegionsHelpers | Helper functions for selectAlnRegions |
| selectOps | 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... |
| transformAlnsToLong | Transform data for plotting |
| variantCounts | Get variant counts |
| writeFastq | Append a sequence to a fastq file |
