modify {RNAmodR} | R Documentation |
SequenceData
The modify
function executes the search for modifications for a
Modifier
class. Usually this is done
automatically during construction of a Modifier
object.
When the modify
functions is called, the aggregated data is checked
for validity for the current settings and the search for modifications is
performed using the findMod
. The results are stored in the
modification
slot of the Modifier
object, which is returned by
modify
. The results can be accessed via the modifications()
function.
findMod
returns the found modifications as a GRanges
object and has to be implemented for each individual Modifier
class.
modifications(x, ...) modify(x, ...) findMod(x) ## S4 method for signature 'Modifier' modifications(x, perTranscript = FALSE) ## S4 method for signature 'Modifier' modify(x, force = FALSE) ## S4 method for signature 'Modifier' findMod(x) ## S4 method for signature 'ModifierSet' modify(x, force = FALSE)
x |
a |
... |
additional arguments |
perTranscript |
For |
force |
force to run |
modify
: the updated Modifier
object.
modifications
: the modifications found as a GRanges
object.
data(msi,package="RNAmodR") # modify() triggers the search for modifications in the data contained in # the Modifier or ModifierSet object mi <- modify(msi[[1]])