Accessory Methods for Analysis of Nanopore Data using R

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Documentation for package ‘nanopoRe’ version 0.2.5

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