Man pages for sagrudd/nanopoRe
Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data
| addCachedYAMLValue | add a stored parameter value for the named config field |
| 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 |
| buildPositionMap | prepares a matrix of operations and coordinates from a CIGAR |
| cachedYAMLToYAML | export the stored config parameters parsed from YAML file |
| chromosomeMappingSummary | prepare mapping summary information by chromosome |
| cigarQ2Op | extracts cigar operations based on query coordinates |
| cigarQ2R | maps query coordinates to the reference sequence |
| cigarR2Op | extracts cigar operations based on reference coordinates |
| cigarR2Q | maps reference coordinates back to the query sequence |
| cleanReferenceGenome | cleanup the reference genome data |
| enrichmentCoverageTypeOverChromosomes | prepare a barchart showing number of bases per chromosome... |
| enrichmentExecutiveSummary | prepare executive summary infographic for the cas9 tutorial |
| enrichmentGetTargetList | return list of defined cas9 target regions |
| enrichmentMappingByGenomicSegment | prepare a table of cas9 target mapping types |
| enrichmentMultiGeneCoveragePanel | prepare a plot of depth-of-coverage across each of the... |
| enrichmentOffTargetKaryogram | prepare a karyogram shaded with regions of off-target mapping |
| enrichmentOffTargetTable | prepare a table of cas9 off-target mapping locations |
| enrichmentSingleTargetPlot | prepare a plot of sequence coverage over a cas9 target region |
| enrichmentStrandedTargetPlot | prepare a plot of sequence coverage shaded by strand over a... |
| enrichmentTargetPerformanceTable | summarise cas9 target performance |
| enrichmentWriteExcelOffTarget | write summary of off-target mapping results to an excel... |
| enrichmentWriteExcelOnTarget | write summary of on-target mapping results to an excel format... |
| extract5mC | prepares a data.frame of per-read methylC bases from provided... |
| extract5mCProbabilities | prepares a data.frame of per-read methylC probability counts |
| extractMethylatedBases | prepares a data.frame of read mapping context for methylation... |
| 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) |
| getCachedYAMLFields | list the parameter fields stored in a cached YAML config file |
| getCachedYAMLValue | get the stored parameter value from named field |
| getChromosomeIds | get chromosome identifiers from reference genome |
| getChromosomeSequence | returns a DNAStringSet object corresponding to specified... |
| getFastqBases | return the number of fastq bases previously parsed from... |
| getFastqCount | return the number of fastq entries previously parsed from... |
| getFastqPlusErrorCount | count of fastq elements rejected due to line 3 plus separator |
| getFlongleChannelMap | produce the channelMap for a flongle flowcell for spatial... |
| getGitDescription | get git metadata for current project |
| getMalformedFastqHeaderCount | count of fastq elements rejected due to malformed fastq... |
| getMinIONChannelMap | produce the channelMap for a MinION flowcell for spatial... |
| getOutputFormat | get the defined output format for ggplot2 figures |
| getPlotDimensions | return defined dimensions for an allowed ggplot2 object |
| getPromethIONChannelMap | produce the channelMap for a PromethION flowcell for spatial... |
| getReferenceGenome | get path reference genome object |
| getReferenceGenomeGR | returns a GRanges object corresponding to the currently... |
| 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... |
| getSkippedLineCount | count of lines of fastq file skipped to enable fastq entry... |
| getStringSetId | accessory method for mapping named chromosomes to their... |
| getZeroLengthSequenceCount | count of fastq elements rejected due to zero length sequence |
| ggbiosave | save a ggbio plot to file |
| hasCachedYAMLField | check for available named cas9 parameter field |
| importConfigYAML | import the cas9 parameters from YAML file |
| importEnrichmentResults | imports the R target output generated by the... |
| 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 |
| isEnrichmentAnalysisComplete | accessory method to test whether the cas9 data indexing has... |
| isInitialised | check nanopoRe environment |
| lcalc | calculate Lstatistics (e.g. L50) for given sequence... |
| LeftRightPlot | plot two ggplot2 figures side by side |
| listCachedObjects | list objects that are stored within the nanopoRe working... |
| listOutputFormat | list available output frameworks for ggplot2 figures |
| loadMethylationBamFile | prepares a data.frame of read mapping context for methylation... |
| loadReferenceGenome | load reference genome into memory |
| md5sum | calculate md5sum checksum for qualified file |
| nanopoRe | nanopoRe |
| ncalc | calculate Nstatistics (e.g. N50) for given sequence... |
| parallelBamSummarise | summarise mapping observations from a BAM file using parallel... |
| 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... |
| RunEnrichmentAnalysis | perform an R-based enrichment analysis for a target region of... |
| SequenceSummaryBarcodeHistogram | present a histogram of read count by sorted barcode Id |
| SequenceSummaryBarcodeInfoGraphic | presents an emojifont based infographic for barcode... |
| SequenceSummaryBarcodeTable | tabulate information on the SequencingSummary barcode fields... |
| SequenceSummaryBasicInfoPlot | present an infographic styled basic characteristics plot of... |
| SequenceSummaryExecutiveSummary | present an infographic styled executive summary of... |
| SequencingSummaryActiveChannelPlot | plot number of observed channels actively producing data... |
| SequencingSummaryBarcodeMerge | merge sequencing summary and barcode summary files |
| SequencingSummaryBase50 | calculates the fractional number of bases according to... |
| SequencingSummaryChannelActivity | prepare a channel activity plot from sequencing_summary reads... |
| SequencingSummaryCumulativeBases | plot cumulative volumes of sequence bases |
| SequencingSummaryCumulativeReads | plot cumulative volumes of sequence reads |
| SequencingSummaryExtractRuntime | from sequencing_summary.txt return integer describing runtime... |
| SequencingSummaryFlowCellID | get flowcell id from sequencing_summary file |
| SequencingSummaryGetPlatform | identify the most likely sequencing platform used to create... |
| SequencingSummaryHasBarcodeInfo | does the SequencingSummary information define a barcode? |
| 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... |
| SequencingSummaryT50 | calculates the timepoint within a sequencing run where... |
| SequencingSummaryTemporalThroughput | plot a sequence throughput against time for specified... |
| SequencingSummaryWeightedReadLength | plot a weighted histogram of sequence read lengths |
| setCachedYAMLValue | update the stored parameter value from named config field |
| 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 |
| svLengthDistribution | prepare figure of SV length distribution |
| SVMappingCharacteristicTable | ont_tutorial_sv = summarise the mapping characteristics from... |
| 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 |
