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.

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

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

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

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

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

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

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

# S4 method for class '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

Value

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")

Examples

data(msi,package="RNAmodR")
mi <- msi[[1]]
settings(mi)
#> $minCoverage
#> [1] 10
#> 
#> $minReplicate
#> [1] 1
#> 
#> $find.mod
#> [1] TRUE
#> 
#> $minScore
#> [1] 0.4
#> 
if (FALSE) { # \dontrun{
aggregate(mi)
modify(mi)
} # }
getDataTrack(mi, "1", mainScore(mi))
#> $score
#> DataTrack 'Score Inosine'
#> | genome: NA
#> | active chromosome: chr1
#> | positions: 1800
#> | samples:1
#> | strand: + 
#>