amplicanMap: Map events to their respective relative coordinates specified...
In amplican: Automated analysis of CRISPR experiments

Description Usage Arguments Value See Also Examples

Translate coordinates of GRanges events so that they can be relative to the amplicon. As point zero we assume first left sided UPPER case letter in the amplicon. Be weary that events for amplicons without expected cut sites are filtered. Don't use this function, if you don't have expected cut sites specified and don't use any of the metaplots.

1	amplicanMap(aln, cfgT)

`aln`	(data.frame) List of events to map to the relative coordinates.
`cfgT`	(data.frame) config table

(GRanges) Same as events, but the coordinates are relative to the expected cut sites.

Other analysis steps: amplicanAlign, amplicanConsensus, amplicanFilter, amplicanNormalize, amplicanOverlap, amplicanPipelineConservative, amplicanPipeline, amplicanReport, amplicanSummarize

# example config
config <- read.csv(system.file("extdata", "config.csv",
                   package = "amplican"))
# example events
events <- read.csv(system.file("extdata", "results", "alignments",
                   "raw_events.csv", package = "amplican"))
# make events relative to the UPPER case
amplicanMap(events, config)