ModInosine-functions: Functions for ModInosine

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

Description

All of the functions of Modifier and the ModifierSet classes are inherited by the ModInosine and ModSetInosine classes.

Check below for the specifically implemented functions.

Usage

## S4 replacement method for signature 'ModInosine'
settings(x) <- value

## S4 method for signature 'ModInosine'
aggregateData(x)

## S4 method for signature 'ModInosine'
findMod(x)

## S4 method for signature 'ModInosine'
getDataTrack(x, name, type, ...)

## S4 method for signature 'ModInosine,GRanges'
plotDataByCoord(x, coord, type = "score", window.size = 15L, ...)

## S4 method for signature 'ModInosine'
plotData(x, name, from = 1L, to = 30L, type = "score", ...)

## S4 method for signature 'ModSetInosine,GRanges'
plotDataByCoord(x, coord, type = "score", window.size = 15L, ...)

## S4 method for signature 'ModSetInosine'
plotData(x, name, from = 1L, to = 30L, type = "score", ...)

Arguments

x	a Modifier or a ModifierSet object. For more details see also the man pages for the functions mentioned below.
value	See settings
coord, name, from, to, type, window.size, ...	See plotData

Details

ModInosine specific arguments for plotData:

• colour.bases - a named character vector of length = 4 for the colours of the individual bases. The names are expected to be c("G","A","U","C")

Value

• settings See settings.

• aggregate See aggregate.

• modify See modify.

• getDataTrack a list of DataTrack objects. See plotDataByCoord.

• plotData See plotDataByCoord.

• plotDataByCoord See plotDataByCoord.

Examples

data(msi,package="RNAmodR")
mi <- msi[[1]]
settings(mi)
## Not run: 
aggregate(mi)
modify(mi)

## End(Not run)
getDataTrack(mi, "1", mainScore(mi))

RNAmodR documentation built on Dec. 15, 2020, 2 a.m.