amplicanSummarize {amplican} | R Documentation |
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
.
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)