Functions for ModAlkAnilineSeq

Description

All of the functions of Modifier and the ModifierSet classes are inherited by the ModAlkAnilineSeq and ModSetAlkAnilineSeq classes.

Usage

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

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

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

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

## S4 method for signature 'ModAlkAnilineSeq,GRanges'
plotDataByCoord(
  x,
  coord,
  type = c("ends", "scoreNC", "scoreSR"),
  window.size = 15L,
  ...
)

## S4 method for signature 'ModAlkAnilineSeq'
plotData(
  x,
  name,
  from = 1L,
  to = 30L,
  type = c("ends", "scoreNC", "scoreSR"),
  ...
)

## S4 method for signature 'ModSetAlkAnilineSeq,GRanges'
plotDataByCoord(
  x,
  coord,
  type = c("scoreNC", "scoreSR", "ends"),
  window.size = 15L,
  ...
)

## S4 method for signature 'ModSetAlkAnilineSeq'
plotData(
  x,
  name,
  from = 1L,
  to = 30L,
  type = c("scoreNC", "scoreSR", "ends"),
  ...
)

Arguments

Details

ModAlkAnilineSeq 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("scoreNC","scoreSR")

Value

• settings See settings.

• aggregate See aggregate.

• modify See modify.

• getDataTrack a list of DataTrack object.

• plotData See plotDataByCoord.

• plotDataByCoord See plotDataByCoord.

Examples

data(msaas,package="RNAmodR.AlkAnilineSeq")
maas <- msaas[[1]]
settings(maas)
aggregate(maas)
modify(maas)
getDataTrack(maas, "1", mainScore(maas))