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

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)
library(nanopoRe)
library(knitr)
library(emojifont)
init()
setOutputFormat("file")

Parsing of configuration file

The cas9-mediated target enrichment workflow is configured by a YAML format file that provides paths to the required files, and parameters specific to the workflow. The YAML file should be loaded and evaluated

yamlFile <- system.file("extdata", "cas9_demo.yaml", package = "nanopoRe")
importConfigYAML(yamlFile=yamlFile)

Since we are operating within a vignette - or out of the expected CONDA/Snakemake environment a manual update for a couple of fields makes sense

unmappedQ <- system.file("extdata", "cas9_FAK76554.unmapped.quals", 
    package = "nanopoRe")
bamFile <- system.file("extdata", "cas9_FAK76554.bam", package = "nanopoRe")
referenceGenome <- system.file("extdata", "cas9_demo_ref.fasta", 
    package = "nanopoRe")
bedTargets <- system.file("extdata", "cas9_demo_target.bed", 
    package = "nanopoRe")

setCachedYAMLValue(field="reference_genome", value=referenceGenome)
setCachedYAMLValue(field="target_regions", value=bedTargets)
addCachedYAMLValue(field="bam_file", value=bamFile)
addCachedYAMLValue(field="unmapped_quals", value=unmappedQ)

cachedYAMLToYAML(format="Kable")

Our ducks should now be lined up for further analysis and exploration ...

Ensure that the enrichment analysis has been run

RunEnrichmentAnalysis(force=TRUE, mc.cores=1)

This can also be validated with the isEnrichmentAnalysisComplete() command

isEnrichmentAnalysisComplete()

importEnrichmentResults()

include_graphics( enrichmentExecutiveSummary() )

enrichmentMappingByGenomicSegment()

enrichmentTargetPerformanceTable()

enrichmentWriteExcelOnTarget()

targets <- enrichmentGetTargetList()
include_graphics( enrichmentSingleTargetPlot(targets[[1]]))

include_graphics( enrichmentStrandedTargetPlot(targets[[1]]) )

include_graphics( enrichmentMultiGeneCoveragePanel() )

include_graphics( enrichmentCoverageTypeOverChromosomes() )

include_graphics( enrichmentOffTargetKaryogram() )

enrichmentOffTargetTable()

enrichmentWriteExcelOffTarget()

The end ...

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