Searching for modifications in 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 class 'Modifier'
modifications(x, perTranscript = FALSE)

# S4 method for class 'Modifier'
modify(x, force = FALSE)

# S4 method for class 'Modifier'
findMod(x)

# S4 method for class 'ModifierSet'
modify(x, force = FALSE)

Arguments

x

a Modifier object.

...

additional arguments

perTranscript

For modifications> TRUE or FALSE: Should the coordinates be returned as local per transcript coordinates?

force

force to run aggregate again, if data is already stored in x.

Value

• modify: the updated Modifier object.

• modifications: the modifications found as a GRanges object.

Examples

data(msi,package="RNAmodR")
# modify() triggers the search for modifications in the data contained in
# the Modifier or ModifierSet object
mi <- modify(msi[[1]])