separate {Modstrings} | R Documentation |
XString
and a GRanges
objectWith 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 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)
x |
For For |
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". (
|
gr |
a GRanges object |
with.qualities |
|
quality.type |
the type of |
stop.on.error |
For |
verbose |
For |
... |
|
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 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)