QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects

title

QualityScaledModDNAStringSet(x, quality)

QualityScaledModRNAStringSet(x, quality)

readQualityScaledModDNAStringSet(
  filepath,
  quality.scoring = c("phred", "solexa", "illumina"),
  nrec = -1L,
  skip = 0L,
  seek.first.rec = FALSE,
  use.names = TRUE
)

readQualityScaledModRNAStringSet(
  filepath,
  quality.scoring = c("phred", "solexa", "illumina"),
  nrec = -1L,
  skip = 0L,
  seek.first.rec = FALSE,
  use.names = TRUE
)

writeQualityScaledModStringSet(
  x,
  filepath,
  append = FALSE,
  compress = FALSE,
  compression_level = NA
)

Arguments

x

For the QualityScaled*StringSet constructors: Either a character vector, or an ModString, ModStringSet or ModStringViews object.

For writeQualityScaledXStringSet: A QualityScaledModDNAStringSet or QualityScaledModRNAStringSet object.

quality

A XStringQuality object.

filepath, nrec, skip, seek.first.rec, use.names, append, compress, compression_level

See QualityScaledXStringSet-class.

quality.scoring

Specify the quality scoring used in the FASTQ file. Must be one of "phred" (the default), "solexa", or "illumina". If set to " phred" (or "solexa" or "illumina"), the qualities will be stored in a PhredQuality (or SolexaQuality or IlluminaQuality, respectively) object.

Value

a QualityScaledModDNAStringSet or QualityScaledModDNAStringSet object

Examples

seq <- ModRNAString("AGCU7")
seq
#> 5-letter ModRNAString object
#> seq: AGCU7

qseq <- PhredQuality(paste0(rep("!", length(seq)), collapse = ""))
qseq
#> PhredQuality object of length 1:
#>     width seq
#> [1]     5 !!!!!

qset <- QualityScaledModRNAStringSet(seq, qseq)
qset
#>   A QualityScaledModRNAStringSet instance containing:
#> 
#>   A ModRNAStringSet instance of length 1
#>     width seq
#> [1]     5 AGCU7
#> 
#> PhredQuality object of length 1:
#>     width seq
#> [1]     5 !!!!!
#>