# Tools for counting and visualising mutations in a target location

## Documentation for package ‘CrispRVariants’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.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