amplican_print_reads: Pretty print forward and reverse reads aligned to each other.

In valenlab/amplican: Automated analysis of CRISPR experiments

Pretty print forward and reverse reads aligned to each other.

Description

Usefull and needed for barcode reports.

Usage

amplican_print_reads(forward, reverse)

Arguments

forward	(character or vector of characters) Forward reads.
reverse	(character or vector of characters) Will be reverse complemented before alignment.

Value

Vector with alignments ready to be printed.

Examples

# load example data
unassigned_file <- system.file('extdata', 'results',  'alignments',
                               'unassigned_reads.csv', package = 'amplican')
unassigned <- data.table::setDF(data.table::fread(unassigned_file))
# sort by frequency
unassigned <- unassigned[order(unassigned$BarcodeFrequency,
                               decreasing = TRUE), ]
# print alignment of most frequent unassigned reads
cat(amplican_print_reads(unassigned[1, 'Forward'],
                         unassigned[1, 'Reverse']),
          sep = "\n")

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