amplicanMap {amplican} | R Documentation |
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.
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)