separate {Modstrings}R Documentation

Separating and combining a ModString object into/from a XString and a GRanges object

Description

With combineIntoModstrings and separate the construction and deconstruction of ModString Objects from an interacive session avoiding problematic encoding issues. In addition, modification information can be transfered from/to tabular data with these functions.

combineIntoModstrings expects seqnames(gr) or names(gr) to match the available names(x). Only information with strand information * and + are used.

Usage

separate(x, nc.type = "short")

combineIntoModstrings(x, gr, with.qualities = FALSE,
  quality.type = "Phred", verbose = FALSE, ...)

## S4 method for signature 'ModString'
separate(x, nc.type = c("short", "nc"))

## S4 method for signature 'ModStringSet'
separate(x, nc.type = c("short", "nc"))

## S4 method for signature 'XString,GRanges'
combineIntoModstrings(x, gr,
  with.qualities = FALSE, quality.type = "Phred", verbose = FALSE,
  ...)

## S4 method for signature 'XStringSet,GRangesList'
combineIntoModstrings(x, gr,
  with.qualities = FALSE, quality.type = "Phred", verbose = FALSE,
  ...)

## S4 method for signature 'XStringSet,GRanges'
combineIntoModstrings(x, gr,
  with.qualities = FALSE, quality.type = "Phred", verbose = FALSE,
  ...)

Arguments

x

For separate: a ModString or ModStringSet object

For combineIntoModstrings: a XStringSet and a GRanges object.

nc.type

the type of nomenclature to be used. Either "short" or "nc". "Short" for m3C would be "m3C", "nc" for m3C would be "3C". ( default = "short")

gr

a GRanges object

with.qualities

TRUE or FALSE (default): Should the values from a score column of the GRanges object stored? If set with.qualities = TRUE, combineIntoModstrings will try to construct a QualityScaledModStringSet object.

quality.type

the type of QualityXStringSet used, if with.qualities = TRUE. Must be on of the following values: "Phred","Solexa","Illumina".

verbose

For combineIntoModstrings: TRUE or FALSE (default): Should verbose information reported on the positions filled with modifications? This settings is passed onto modifyNucleotides.

...

  • default.quality: For combineIntoModstrings: the default.quality default value for non-modified positions. (default: default.quality = 0L)

Value

for separate a GRanges object and for combineIntoModstrings a ModString* object or a QualityScaledModStringSet, if with.qualities = TRUE.

Examples

seq <- ModDNAString(paste(alphabet(ModDNAString()), collapse = ""))
gr <- separate(seq)
seq <- combineIntoModstrings(as(seq,"DNAString"),gr)
[Package Modstrings version 1.0.3 Index]