QualityScaledModStringSet: QualityScaledModDNAStringSet and QualityScaledModRNAStringSet...

In FelixErnst/Modstrings: Working with modified nucleotide sequences

QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects

Description

title

Usage

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

qseq <- PhredQuality(paste0(rep("!", length(seq)), collapse = ""))
qseq

qset <- QualityScaledModRNAStringSet(seq, qseq)
qset

FelixErnst/Modstrings documentation built on April 1, 2024, 2:21 p.m.