check_encoding: Check quality encoding

In FastqCleaner: A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files

Description

Check quality encoding

Usage

check_encoding(x = NULL, custom = NULL)

Arguments

x	Quality values
custom	custom encoding from the following: 'Sanger' ——–> expected range: [0, 40] 'Illumina1.8' ——–> expected range: [0, 41] 'Illumina1.5' ——–> expected range: [0, 40] 'Illumina1.3' ——–> expected range: [3, 40] 'Solexa' ——–> expected range: [-5, 40]

Value

List with encoding information

Author(s)

Leandro Roser [e-mail]

Examples

require(Biostrings)

x <- list(PhredQuality(0:40), SolexaQuality(-5:40), IlluminaQuality(3:40))
x <- lapply(x, function(i)utf8ToInt(as.character(i)[1]))
lapply(x, check_encoding)
 
SolexaQuality(0:40)
IlluminaQuality(0:40)

FastqCleaner documentation built on Nov. 8, 2020, 5:05 p.m.