Tools for counting and visualising mutations in a target location


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Documentation for package ‘CrispRVariants’ version 1.4.1

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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
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
gol Variant sequences from golden clutch 1 (Burger et al)
gol_clutch1 Variant sequences from golden clutch 1 (Burger et al)
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
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
seqsToAln Creates a text alignment from a set of cigar strings
setDNATileColours Sets colours for plotting 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