findLQR {amplican} | R Documentation

## 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)

[Package amplican version 1.16.0 Index]