separate {Modstrings} | R Documentation |
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(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, ...)
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 |
verbose |
For |
... |
|
for separate
a GRanges
object and for
combineIntoModstrings
a ModString*
object or a
QualityScaledModStringSet
, if with.qualities = TRUE
.
seq <- ModDNAString(paste(alphabet(ModDNAString()), collapse = "")) gr <- separate(seq) seq <- combineIntoModstrings(as(seq,"DNAString"),gr)