check_encoding.Rd
Check quality encoding
check_encoding(x = NULL, custom = NULL)
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] |
List with encoding information
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)#> [[1]] #> [[1]]$x #> [1] "Sanger" #> #> [[1]]$y #> [1] 1 #> #> [[1]]$q #> [1] 33 #> #> [[1]]$range #> [1] "[33 - 73]" #> #> #> [[2]] #> [[2]]$x #> [1] "Solexa" #> #> [[2]]$y #> [1] 5 #> #> [[2]]$q #> [1] 64 #> #> [[2]]$range #> [1] "[59; 104]" #> #> #> [[3]] #> [[3]]$x #> [1] "Illumina 1.5+" #> #> [[3]]$y #> [1] 3 #> #> [[3]]$q #> [1] 64 #> #> [[3]]$range #> [1] "[66; 104]" #> #>#> A SolexaQuality instance of length 1 #> width seq #> [1] 41 @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh#> A IlluminaQuality instance of length 1 #> width seq #> [1] 41 @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh