amplicanMap: Map events to their respective relative coordinates specified...

In valenlab/amplican: Automated analysis of CRISPR experiments

Map events to their respective relative coordinates specified with UPPER case.

Description

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.

Usage

amplicanMap(aln, cfgT)

Arguments

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

Value

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

See Also

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

Examples

# 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)

valenlab/amplican documentation built on Jan. 28, 2024, 5:10 a.m.