amplicanSummarize {amplican} | R Documentation

## Summarize how many reads have frameshift and how many reads have deletions.

### Description

Before using this function make sure events are filtered to represent consensus with `amplicanConsensus`, if you use both forward and reverse reads. If you want to calculate metrics over expected cut site, filter events using `amplicanOverlap`.

### Usage

    amplicanSummarize(aln, cfgT)

### Arguments

`aln` | (data.frame) Contains events from the alignments.
`cfgT` | (data.frame) Config file with the experiments details.

### Details

Adds columns to cfgT:

- ReadsCut Count of reads with deletions overlapping expected cut site.

- Reads_Frameshifted Count of reads with frameshift overlapping expected cut site.

### Value

(data.frame) As cfgT, but with extra columns.

### See Also

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

### Examples

    file_path <- system.file("extdata", "results", "alignments",
                             "events_filtered_shifted_normalized.csv",
                             package = "amplican")
    aln <- data.table::fread(file_path)
    cfgT <- data.table::fread(
      system.file("extdata", "results", "config_summary.csv",
                  package = "amplican"))
    amplicanSummarize(aln, cfgT)

[Package amplican version 1.10.1 Index]