Accessory Methods for the Analysis of Oxford Nanopore
Technologies DNA Sequence Data
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Documentation for package ‘nanopoRe’ version 0.2.9
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 |