amplicanSummarize: Summarize how many reads have frameshift and how many reads...
In amplican: Automated analysis of CRISPR experiments

Description Usage Arguments Details Value See Also Examples

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.

1	amplicanSummarize(aln, cfgT)

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

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

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

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)