RunEnrichmentAnalysis: perform an R-based enrichment analysis for a target region of...

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

Description

This method is associated with the cas9-mediated enrichment of genomic target regions ...

Usage

RunEnrichmentAnalysis(force = FALSE, ...)

Arguments

force	defines whether a reanalysis of the data should be forced if results already existing
...	- who knows - I'm using this for mc.cores

Value

TRUE or FALSE depending

Examples

yamlFile <- system.file("extdata", "cas9_demo.yaml", package = "nanopoRe")
importConfigYAML(yamlFile=yamlFile)
isEnrichmentAnalysisComplete()
# this is a header to a document - not a live Snakemake workspace - demo
# how to actually run ad-hoc the code
setCachedYAMLValue(
    field="reference_genome",
    value=system.file("extdata", "cas9_demo_ref.fasta", package="nanopoRe"))
setCachedYAMLValue(
    field="target_regions",
    value=system.file("extdata", "cas9_demo_target.bed", package="nanopoRe"))
addCachedYAMLValue(
    field="bam_file",
    value=system.file("extdata", "cas9_FAK76554.bam", package ="nanopoRe"))
addCachedYAMLValue(
    field="unmapped_quals",
    value=system.file("extdata", "cas9_FAK76554.unmapped.quals",
    package="nanopoRe"))
# lines between the previous comment and here are typically not required
RunEnrichmentAnalysis(mc.cores=1)

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