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

In Modstrings: Working with modified nucleotide sequences

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)

Modstrings documentation built on Nov. 8, 2020, 7:51 p.m.