# Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data

## Documentation for package ‘nanopoRe’ version 0.2.9

- DESCRIPTION file.
- Package NEWS.

## Help Pages

bamSummarise | summarise mapping observations from a BAM file
bamSummariseByChr | summarise mapping observations from a BAM file by chromosome
bamSummaryToCoverage | get depth of coverage information from across the genome
cas9CoverageTypeOverChromosomes | prepare a barchart showing number of bases per chromosome coloured by mapping-type
cas9ExecutiveSummary | prepare executive summary infographic for the cas9 tutorial
cas9GetTargetList | return list of defined cas9 target regions
cas9MappingByGenomicSegment | prepare a table of cas9 target mapping types
cas9MultiGeneCoveragePanel | prepare a plot of depth-of-coverage across each of the cas9-enrichment targets included in study
cas9OffTargetKaryogram | prepare a karyogram shaded with regions of off-target mapping
cas9OffTargetTable | prepare a table of cas9 off-target mapping locations
cas9SingleTargetPlot | prepare a plot of sequence coverage over a cas9 target region
cas9StrandedTargetPlot | prepare a plot of sequence coverage shaded by strand over a cas9 target region
cas9TargetPerformanceTable | summarise cas9 target performance
cas9WriteExcelOffTarget | write summary of off-target mapping results to an excel format result file
cas9WriteExcelOnTarget | write summary of on-target mapping results to an excel format result file
chromosomeMappingSummary | prepare mapping summary information by chromosome
cleanReferenceGenome | cleanup the reference genome data
fastqCheckup | perform a sanity check and prepare summary info on fastq file
fastqValidator | parse a fastq file aiming to validate sequences
fixFastq | fix a corrupted fastq file (if fastq-like)
getChromosomeIds | get chromosome identifiers from reference genome
getChromosomeSequence | returns a DNAStringSet object corresponding to specified chromosome from reference genome
getFastqBases | return the number of fastq bases previously parsed from provided Fastq file
getFastqCount | return the number of fastq entries previously parsed from provided Fastq file
getFastqPlusErrorCount | count of fastq elements rejected due to line 3 plus separator
getFlongleChannelMap | produce the channelMap for a flongle flowcell for spatial plots
getMalformedFastqHeaderCount | count of fastq elements rejected due to malformed fastq header
getMinIONChannelMap | produce the channelMap for a MinION flowcell for spatial plots
getOutputFormat | get the defined output format for ggplot2 figures
getPlotDimensions | return defined dimensions for an allowed ggplot2 object
getReferenceGenome | get path reference genome object
getRpath | get path for R results
getSeqLengths | get chromosome lengths for a named set of chromosomes
getSequenceQualityMismatchCount | count of fastq elements rejected due to mismatch between sequence and quality field lengths
getSkippedLineCount | count of lines of fastq file skipped to enable fastq entry parsing
getStringSetId | accessory method for mapping named chromosomes to their pointers in the reference fasta
getZeroLengthSequenceCount | count of fastq elements rejected due to zero length sequence
ggbiosave | save a ggbio plot to file
importCas9TutorialData | imports the R target output generated by the ont_tutorial_cas9 workflow
importSequencingSummary | load a sequencing_summary.txt file into memory
infoGraphicPlot3 | prepare an 3x infographic-styled summary plot
infoGraphicPlot4 | prepare a 4x infographic-styled summary plot
infoGraphicPlot5 | prepare a 5x infographic-styled summary plot
init | Initialise the nanopoRe environment
isInitialised | check nanopoRe environment
lcalc | calculate Lstatistics (e.g. L50) for given sequence collection
LeftRightPlot | plot two ggplot2 figures side by side
listCachedObjects | Initialise the NanopoRe environment
listOutputFormat | list available output frameworks for ggplot2 figures
loadReferenceGenome | load reference genome into memory
md5sum | calculate md5sum checksum for qualified file
ncalc | calculate Nstatistics (e.g. N50) for given sequence collection
parallelBamSummarise | summarise mapping observations from a BAM file using parallel chr-by-chr
phredmean | calculate mean Phred scores from list of Q values
plotAlignmentAccuracy | plot a histogram of mapping accuracies
plotAlignmentIdentity | plot a histogram of mapping identities
plotDepthOfCoverageMegablock | plot a tiled panel of chromosomal depths-of-coverage
plotOverallCovHistogram | plot a histogram of whole genome depth-of-coverage
qualToMeanQ | calculate mean Phred score from an ASCII encoded phred string
RepeatMaskerGR | extract GRanges object corresponding to RepeatMasker annotation
SequenceSummaryBarcodeHistogram | present a histogram of read count by sorted barcode Id
SequenceSummaryBarcodeInfoGraphic | presents an emojifont based infographic for barcode characteristics
SequenceSummaryBarcodeTable | tabulate information on the SequencingSummary barcode fields and status
SequenceSummaryBasicInfoPlot | present an infographic styled basic characteristics plot of sequence_summary.txt content
SequenceSummaryExecutiveSummary | present an infographic styled executive summary of sequence_summary.txt content
SequencingSummaryActiveChannelPlot | plot number of observed channels actively producing data against time
SequencingSummaryBarcodeMerge | calculates the fractional number of bases according to supplied b parameter
SequencingSummaryBase50 | calculates the fractional number of bases according to supplied b parameter
SequencingSummaryChannelActivity | prepare a channel activity plot from sequencing_summary reads file
SequencingSummaryCumulativeBases | plot cumulative volumes of sequence bases
SequencingSummaryCumulativeReads | plot cumulative volumes of sequence reads
SequencingSummaryGetPlatform | identify the most likely sequencing platform used to create the summary data
SequencingSummaryPassGauge | prepare a gauge plot of sequencing_summary reads passing QC
SequencingSummaryReadLengthHistogram | plot a histogram of sequence read lengths
SequencingSummaryReadLengthQualityDensity | plot a density map of sequence lengths and quality scores
SequencingSummaryReadQualityHistogram | plot a histogram of sequence quality scores
SequencingSummarySpeedPlot | plot speed of sequencing against time (bases per second distribution)
SequencingSummaryT50 | calculates the timepoint within a sequencing run where 50percent of the data is produced
SequencingSummaryTemporalThroughput | plot a sequence throughput against time for specified sequencing_summary run
SequencingSummaryWeightedReadLength | plot a weighted histogram of sequence read lengths
setLogFile | method to mask R output by writing to a log file
setOutputFormat | set the defined output format for ggplot2 figures
setPlotDimensions | set dimension definitions for an allowed ggplot2 object
setReferenceGenome | set path for reference genome object
setRpath | set path for R results
snifflesKaryogram | prepare karyogram of annotated SVs
sourceCas9Parameters | import the cas9 parameters from YAML file
svLengthDistribution | prepare figure of SV length distribution
SVMappingCharacteristicTable | ont_tutorial_sv = summarise the mapping characteristics from a given BAM file
testBam | extract content from a BAM file
unsetLog | method to output capture to log file
Vcf2FilteredGranges | extract SV variants from a sniffles VCF file by SVTYPE
Vcf2GRanges | convert VCF content into a GRanges object for nanopoRe usage