amplicanMap {amplican} | R Documentation

## 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)

[Package amplican version 1.16.0 Index]