combineFragEnds {FourCSeq} | R Documentation

## Combine the counts of both fragment ends.

### Description

`combineFragEnds` combines the counts of both fragment ends. A multiplication factor can be used for fragments that only have counts for one valid fragment end.

### Usage

    combineFragEnds(object, multFactor = 1, filter = FALSE)

### Arguments

`object` | A `FourC` object.
`multFactor` | Multiplication factor that can be used to multiply the counts of fragments which only have one valid end. Default is `1`. `filter` is automatically set to `TRUE` if `multFactor` is different from 1.
`filter` | If filter is `TRUE`, only reads from valid fragment ends are summed up for each fragment. This means if only one fragment end is valid only counts from this end are considered. If filter is `FALSE`, counts from both fragment ends are summed up without any filtering.

### Value

Returns an updated `FourC` object with a new assay `counts` containing the combined count data of both fragment ends for all viewpoints.

### Author(s)

Felix A. Klein, felix.klein@embl.de

### See Also

`FourC`, `countFragmentOverlaps`

### Examples

    data(fc, package="FourCSeq")

    fc <- combineFragEnds(fc)
    fc

[Package FourCSeq version 1.21.0 Index]