findLQR: Find Off-targets and Fragmented alignments from reads.

In valenlab/amplican: Automated analysis of CRISPR experiments

Find Off-targets and Fragmented alignments from reads.

Description

Will try to detect off-targets and low quality alignments (outliers). It tries k-means clustering on normalized number of events per read and read alignment score. If there are 3 clusters (decided based on silhouette criterion) cluster with high event count and low alignment score will be marked for filtering. When there is less than 1000 scores in aln it will filter nothing.

Usage

findLQR(aln)

Arguments

aln	(data.frame) Should contain events from alignments in GRanges style with columns eg. seqnames, width, start, end, score.

Value

(logical vector) where TRUE indicates events that are potential off-targets or low quality alignments.

See Also

findPD findEOP

Other filters: findEOP(), findPD()

Examples

file_path <- system.file("extdata", "results", "alignments",
                         "raw_events.csv", package = "amplican")
aln <- data.table::fread(file_path)
aln <- aln[seqnames == "ID_1"] # for first experiment
findLQR(aln)

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