SVMappingCharacteristicTable: ont_tutorial_sv = summarise the mapping characteristics from...

In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data

Description

this method prepares a kable format table summarising the key mapping characteritics from a provided BAM file summary (from bamSummarise). This will describe the mapped sequence reads that are defined as primary, secondary and supplementary and will overlay additional data that releases to read length, read quality and other characteristics as reported in the tutorial document

Usage

SVMappingCharacteristicTable(bamSummary, validationResponse, bamFile)

Arguments

bamSummary	is the result from bamSummarise
validationResponse	is the product of the floundeR fastqCheckup method
bamFile	is a path to a file

Value

kable table of mapping characteristics as tuned for the ont_tutorial_sv document

Examples

demoBam <- system.file("extdata",
    "Ecoli_zymo_R10_filt_subs.bam",
    package = "nanopoRe")
demoFastq <- system.file("extdata",
    "Ecoli_zymo_R10.fastq.gz",
    package = "nanopoRe")
referenceGenome <- system.file("extdata",
    "Escherichia_coli_complete_genome.fasta",
    package = "nanopoRe")
setReferenceGenome(referenceGenome)
loadReferenceGenome()
bamSummary <- bamSummarise(demoBam, force=FALSE, blockSize=1000L)
fastqView <- fastqCheckup(demoFastq)
kable <- SVMappingCharacteristicTable(bamSummary, fastqView, demoBam)

sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.