XString and a GRanges objectR/AllGenerics.R, R/Modstrings-separate.R
separate.RdWith 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.
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 ModString
separate(x, nc.type = c("short", "nc"))
# S4 method for ModStringSet
separate(x, nc.type = c("short", "nc"))
# S4 method for GRanges
separate(x)
# S4 method for GRangesList
separate(x)
# S4 method for XString,GRanges
combineIntoModstrings(
x,
gr,
with.qualities = FALSE,
quality.type = "Phred",
stop.on.error = TRUE,
verbose = FALSE,
...
)
# S4 method for XStringSet,GRangesList
combineIntoModstrings(
x,
gr,
with.qualities = FALSE,
quality.type = "Phred",
stop.on.error = TRUE,
verbose = FALSE,
...
)
# S4 method for XStringSet,GRanges
combineIntoModstrings(
x,
gr,
with.qualities = FALSE,
quality.type = "Phred",
stop.on.error = TRUE,
verbose = FALSE,
...
)
# S4 method for GRanges
combineModifications(gr)
# S4 method for GRangesList
combineModifications(gr)
# S4 method for GRanges,XString
incompatibleModifications(gr, x)
# S4 method for GRanges,XStringSet
incompatibleModifications(gr, x)
# S4 method for GRangesList,XStringSet
incompatibleModifications(gr, x)
# S4 method for GRanges,XString
removeIncompatibleModifications(gr, x)
# S4 method for GRanges,XStringSet
removeIncompatibleModifications(gr, x)
# S4 method for GRangesList,XStringSet
removeIncompatibleModifications(gr, x)For separate: a ModString/ModStringSet or
GRanges/GRangesListobject
For combineIntoModstrings: a XString and a XStringSet
object.
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")
a GRanges object
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.
the type of QualityXStringSet used, if
with.qualities = TRUE. Must be on of the following values:
"Phred","Solexa","Illumina".
For combineIntoModstrings: TRUE(default)
or FALSE: Should an error be raised upon encounter of incompatible
positions?
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)
for separate a GRanges object and for
combineIntoModstrings a ModString* object or a
QualityScaledModStringSet, if with.qualities = TRUE.
library(GenomicRanges)
# ModDNAString
seq <- ModDNAString(paste(alphabet(ModDNAString()), collapse = ""))
seq
#> 55-letter ModDNAString object
#> seq: ACGTN-+.pδO]DJeg`bU∝πI763218∉⊆⊇Rαmh×f4νX'κo()ηa⇓⇑"√/≡ζ~
gr <- separate(seq)
gr
#> GRanges object with 47 ranges and 1 metadata column:
#> seqnames ranges strand | mod
#> <Rle> <IRanges> <Rle> | <character>
#> [1] 1 9 + | 5pT
#> [2] 1 10 + | 3mT
#> [3] 1 11 + | O4meT
#> [4] 1 12 + | 1mT
#> [5] 1 13 + | dhT
#> ... ... ... ... . ...
#> [43] 1 51 + | 6haA
#> [44] 1 52 + | 2mA
#> [45] 1 53 + | 2a6haA
#> [46] 1 54 + | 6,6mA
#> [47] 1 55 + | 6ncmA
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
seq2 <- combineIntoModstrings(as(seq,"DNAString"),gr)
seq2
#> 55-letter ModDNAString object
#> seq: ACGTN-+.pδO]DJeg`bU∝πI763218∉⊆⊇Rαmh×f4νX'κo()ηa⇓⇑"√/≡ζ~
seq == seq2
#> [1] TRUE
# ModRNAString
seq <- ModRNAString(paste(alphabet(ModRNAString()), collapse = ""))
seq
#> 153-letter ModRNAString object
#> seq: ACGUN-+.œεξα"KO]±Γ}/£ÿ≠≈*∞[ω∏%2:B#≤Z...Ϩ≡Ϫ√ΘE=6¿(eDς9⊄«⊆I⊇8y∑WPQšÎ÷H<;ÜVυY€
gr <- separate(seq)
gr
#> GRanges object with 145 ranges and 1 metadata column:
#> seqnames ranges strand | mod
#> <Rle> <IRanges> <Rle> | <character>
#> [1] 1 9 + | m1Am
#> [2] 1 10 + | m1Gm
#> [3] 1 11 + | m1Im
#> [4] 1 12 + | m1acp3Y
#> [5] 1 13 + | m1A
#> ... ... ... ... . ...
#> [141] 1 149 + | xU
#> [142] 1 150 + | cmo5U
#> [143] 1 151 + | mcmo5U
#> [144] 1 152 + | yW
#> [145] 1 153 + | imG
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# Separating RNA modifications
gr <- gr[1]
separate(gr)
#> GRanges object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | mod
#> <Rle> <IRanges> <Rle> | <character>
#> [1] 1 9 + | Am
#> [2] 1 9 + | m1A
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# ... and combine them again (both operations work only on a subset of
# modifications)
combineModifications(separate(gr))
#> GRanges object with 1 range and 1 metadata column:
#> seqnames ranges strand | mod
#> <Rle> <IRanges> <Rle> | <character>
#> [1] 1 9 + | m1Am
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# handling incompatible modifications
seq <- RNAString("AGCU")
gr <- GRanges(c("chr1:1:+","chr1:2:+"),mod="m1A")
incompatibleModifications(gr,seq)
#> [1] FALSE TRUE
#
removeIncompatibleModifications(gr,seq)
#> GRanges object with 1 range and 1 metadata column:
#> seqnames ranges strand | mod
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 1 + | m1A
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths