Description Usage Arguments Value See Also Examples
View source: R/amplicanFilter.R
Very often alignments return deletions that are not real deletions, but
rather artifact of incomplete reads eg.:
1 2 | ACTGAAAAA------- <- this "deletion" should be filtered
ACTG----ACTGACTG
|
We call them Events Overlapping Primers and filter them together with reads that are potentially PRIMER DIMERS. This filter will also remove all events coming from reads with low alignment score - potential Off-targets.
1 | amplicanFilter(aln, cfgT, PRIMER_DIMER)
|
aln |
(data.frame) Should contain events from alignments in GRanges style with columns eg. seqnames, width, start, end. |
cfgT |
(data.frame) Needs columns Forward_Primer, ReversePrimer and Amplicon. |
PRIMER_DIMER |
(numeric) Value specifying buffer for PRIMER DIMER
detection. For a given read it will be recognized as PRIMER DIMER when
alignment will introduce gap of size bigger than: |
(aln) Reduced by events classified as PRIMER DIMER or overlapping primers.
Other analysis steps: amplicanAlign
,
amplicanConsensus
,
amplicanMap
,
amplicanNormalize
,
amplicanOverlap
,
amplicanPipelineConservative
,
amplicanPipeline
,
amplicanReport
,
amplicanSummarize
1 2 3 4 5 6 7 | file_path <- system.file("extdata", "results", "alignments",
"raw_events.csv", package = "amplican")
aln <- data.table::fread(file_path)
cfgT <- data.table::fread(
system.file("extdata", "results", "config_summary.csv",
package = "amplican"))
amplicanFilter(aln, cfgT, 30)
|
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