ModRiboMethSeq-functions: Functions for ModRiboMethSeq

In RNAmodR.RiboMethSeq: Detection of 2'-O methylations by RiboMethSeq

Description

All of the functions of Modifier and the ModifierSet classes are inherited by the ModRiboMethSeq and ModSetRiboMethSeq classes.

Usage

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

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

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

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

## S4 method for signature 'ModRiboMethSeq,GRanges'
plotDataByCoord(
  x,
  coord,
  type = c("ends", "scoreA", "scoreB", "scoreRMS", "scoreMean"),
  window.size = 15L,
  ...
)

## S4 method for signature 'ModRiboMethSeq'
plotData(
  x,
  name,
  from = 1L,
  to = 30L,
  type = c("ends", "scoreA", "scoreB", "scoreRMS", "scoreMean"),
  ...
)

## S4 method for signature 'ModSetRiboMethSeq,GRanges'
plotDataByCoord(
  x,
  coord,
  type = c("scoreRMS", "ends", "scoreA", "scoreB", "scoreMean"),
  window.size = 15L,
  ...
)

## S4 method for signature 'ModSetRiboMethSeq'
plotData(
  x,
  name,
  from = 1L,
  to = 30L,
  type = c("scoreRMS", "ends", "scoreA", "scoreB", "scoreMean"),
  ...
)

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

ModRiboMethSeq specific arguments for plotData:

• colour - a named character vector of length = 4 for the colours of the individual histograms. The names are expected to be c("ends","scoreA","scoreB","scoreRMS","scoreMean")

Value

• settings See settings.

• aggregate See aggregate.

• modify See modify.

• getDataTrack a list of DataTrack object.

• plotData See plotDataByCoord.

• plotDataByCoord See plotDataByCoord.

Examples

data(msrms,package="RNAmodR.RiboMethSeq")
mrms <- msrms[[1]]
settings(mrms)
aggregate(mrms)
modify(mrms)
getDataTrack(mrms, "1", mainScore(mrms))

RNAmodR.RiboMethSeq documentation built on Nov. 8, 2020, 5:45 p.m.