applyMapped: Apply a function over mapped data.
In Genominator: Analyze, manage and store genomic data

Description Usage Arguments Value Author(s) See Also Examples

Apply a function over each element of a list containing data subsets, organized by annotation, with an additional argument for the annotation element associated with the list item.

1	applyMapped(mapped, annoData, FUN, bindAnno = FALSE)

`mapped`	A list of data subsets, typically the return value of a call to `splitByAnnotation`. Names should correspond to names of `annoData` object.
`annoData`	A data frame which must contain the columns `chr`, `start`, `end` and `strand` which specifies annotation regions of interest.
`FUN`	A function of two arguments, the first being an element of `mapped`, the second being the corresponding element of `annoData`.
`bindAnno`	Logical indicating whether annotation information should be included in the output. If `TRUE` it assumes the output of `FUN` is conformable into a `data.frame`.

If bindAnno is FALSE, returns a list containing the output of FUN for each element of the original mapped argument. If bindAnno is TRUE, returns a data frame, containing annotation information and output of FUN.

James Bullard bullard@berkeley.edu, Kasper Daniel Hansen khansen@jhsph.edu

See Genominator vignette for more information.

ed <- ExpData(system.file(package = "Genominator", "sample.db"),
              tablename = "raw")
data("yeastAnno")
s <- splitByAnnotation(ed, yeastAnno[1:100,],
                       what = getColnames(ed, all = FALSE),
                       ignoreStrand = TRUE, addOverStrand = TRUE)

## compute the per-base rate for this dataset.
applyMapped(s, yeastAnno, function(dta, anno) {
   colSums(dta, na.rm = TRUE)/(anno$end - anno$start + 1)
}, bindAnno = TRUE)[1:4,]