# Accessory Methods for Analysis of Nanopore Data using R

## Documentation for package ‘nanopoRe’ version 0.2.5

- DESCRIPTION file.

## 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
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
getMalformedFastqHeaderCount | count of fastq elements rejected due to malformed fastq header
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
infoGraphicPlot3 | prepare an 3x infographic-styled summary plot
infoGraphicPlot4 | prepare a 4x 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
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
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
testBam | extract content from a BAM file
Vcf2FilteredGranges | extract SV variants from a sniffles VCF file by SVTYPE
Vcf2GRanges | convert VCF content into a GRanges object for nanopoRe usage