amplicanSummarize: Summarize how many reads have frameshift and how many reads...

In valenlab/amplican: Automated analysis of CRISPR experiments

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)

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