meltSignals
meltSignals.RdAggregates and melts a list of signal matrices, for plotting (with ggplot).
Arguments
- ml
A named list of signal matrices or an EnrichmentSE object as produced by
signal2Matrix- fun
An optional custom aggregation function (or named list thereof).
- splitBy
A vector of values (factor or character of length equal to `nrow(ml)`) by which to split the aggregation. Can also be the name of a column of `rowData(ml)`.
- trim
The quantile above which to trim values. If a numeric vector of length 2, will be used as lower and upper quantiles beyond which to trim.
- assay
Assay to use (ignored unless `ml` is an ESE object), defaults to the first assay.
Examples
# we first get an EnrichmentSE object:
data(exampleESE)
# we extract the means per position:
d <- meltSignals(exampleESE)
head(d)
#> position sample mean SD SE median
#> 1 -2000 H3K27ac 83.28000 182.5112 14.90197 11.5
#> 2 -1950 H3K27ac 85.87333 189.9628 15.51040 11.5
#> 3 -1900 H3K27ac 91.19333 207.2911 16.92525 9.0
#> 4 -1850 H3K27ac 90.92000 201.2272 16.43013 8.5
#> 5 -1800 H3K27ac 88.02667 192.6586 15.73051 10.0
#> 6 -1750 H3K27ac 85.52000 173.5301 14.16867 14.5
## we could then plot for instance using ggplot:
# ggplot(d, aes(position, mean, colour=sample)) + geom_line(size=1.2)