applyMapped {Genominator} | R Documentation

## Apply a function over mapped data.

### Description

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.

### Usage

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

### Arguments

`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`.

### Value

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`.

### Author(s)

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

### See Also

See `Genominator` vignette for more information.

### Examples

    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,]

[Package Genominator version 1.40.0 Index]