Functions for ModInosine

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 ModInosine
settings(x) <- value

# S4 method for ModInosine
aggregateData(x)

# S4 method for ModInosine
findMod(x)

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

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

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

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

# S4 method for 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

• settings See settings.

• aggregate See aggregate.

• modify See modify.

• getDataTrack a list of DataTrack objects. See plotDataByCoord.

• plotData See plotDataByCoord.

• plotDataByCoord See plotDataByCoord.

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) {
aggregate(mi)
modify(mi)
}
getDataTrack(mi, "1", mainScore(mi))
#> $score
#> DataTrack 'Score Inosine'
#> | genome: NA
#> | active chromosome: chr1
#> | positions: 1800
#> | samples:1
#> | strand: + 
#>