modify: Searching for modifications in 'SequenceData'

In FelixErnst/RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data

Searching for modifications in SequenceData

Description

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.

Usage

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)

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]])

FelixErnst/RNAmodR documentation built on March 27, 2024, 2:42 a.m.