getBarcodeThresholds: Get score thresholds for barcode alignments
In MarioniLab/sarlacc: Pipeline for Oxford Nanopore RNA-Seq Data Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

Compute score thresholds to be used to determine if the read sequence matches a known reference barcode.

1	getBarcodeThresholds(baligned, nmads=3)

`baligned`	A DataFrame of barcode alignment information for each read, identical to the output of `barcodeAlign`.
`nmads`	A numeric scalar specifying the number of median absolute deviations to define outliers.

The threshold for each metric is defined at nmads MADs below the median across all reads. The assumption here is that most reads are aligned to correct barcodes. Any small outliers are considered to represent misalignments and are removed.

A named numeric vector of length 2. This contains score, the threshold on the alignment score; and gap, the threshold on the difference between the best and next-best score.

Aaron Lun

barcodeAlign to generate baligned.