separate: Separating and combining a modification information into/from...

In FelixErnst/Modstrings: Working with modified nucleotide sequences

Separating and combining a modification information 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.

separate when used with a GRanges/GRangesList object will return an object of the same type, but with modifications seperated. For example an element with mod = "m1Am" will be returned as two elements with mod = c("Am","m1A"). The reverse operation is available via combineModifications().

removeIncompatibleModifications filters incompatible modification from a GRanges or GRangesList. incompatibleModifications() returns the logical vector used for this operation.

Usage

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

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

combineModifications(gr, ...)

incompatibleModifications(gr, x, ...)

removeIncompatibleModifications(gr, x, ...)

## 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 'GRanges'
separate(x)

## S4 method for signature 'GRangesList'
separate(x)

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

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

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

## S4 method for signature 'GRanges'
combineModifications(gr)

## S4 method for signature 'GRangesList'
combineModifications(gr)

## S4 method for signature 'GRanges,XString'
incompatibleModifications(gr, x)

## S4 method for signature 'GRanges,XStringSet'
incompatibleModifications(gr, x)

## S4 method for signature 'GRangesList,XStringSet'
incompatibleModifications(gr, x)

## S4 method for signature 'GRanges,XString'
removeIncompatibleModifications(gr, x)

## S4 method for signature 'GRanges,XStringSet'
removeIncompatibleModifications(gr, x)

## S4 method for signature 'GRangesList,XStringSet'
removeIncompatibleModifications(gr, x)

Arguments

x	For separate: a ModString/ModStringSet or GRanges/GRangesListobject For combineIntoModstrings: a XString and a XStringSet 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".
stop.on.error	For combineIntoModstrings: TRUE(default) or FALSE: Should an error be raised upon encounter of incompatible positions?
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

library(GenomicRanges)
# ModDNAString
seq <- ModDNAString(paste(alphabet(ModDNAString()), collapse = ""))
seq

gr <- separate(seq)
gr

seq2 <- combineIntoModstrings(as(seq,"DNAString"),gr)
seq2

seq == seq2
# ModRNAString
seq <- ModRNAString(paste(alphabet(ModRNAString()), collapse = ""))
seq

gr <- separate(seq)
gr

# Separating RNA modifications
gr <- gr[1]
separate(gr)

# ... and combine them again (both operations work only on a subset of
# modifications)
combineModifications(separate(gr))

# handling incompatible modifications
seq <- RNAString("AGCU")
gr <- GRanges(c("chr1:1:+","chr1:2:+"),mod="m1A")
incompatibleModifications(gr,seq)

#
removeIncompatibleModifications(gr,seq)

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