countFragmentOverlapsSecondCutter {FourCSeq} | R Documentation

## Count fragment overlaps when sequencing was performed from the second cutting site

### Description

`countFragmentOverlapsSecondCutter` counts the number of reads mapping to each cutting site of the second cutter and then summarizes them over the fragment ends of the first cutter stored in `rowRanges` of the `FourC` object.

### Usage

    countFragmentOverlapsSecondCutter(
      object,
      extend = TRUE,
      minMapq = 0,
      shift = 0
    )

### Arguments

`object` | A `FourC` object.
`extend` | Defines whether the read start should be extended by the length of the second cutter recognition sequence to overlap the cutting sites which is required for counting. If the cutting site has been trimmed with the primer sequence this has to be set to `TRUE`. Default is `TRUE`.
`minMapq` | Minimum mapping quality required for counting the read. Default is `0`. If set to negative values the filtering step is skipped.
`shift` | Maximum difference in starts or ends between read and fragment positions. Default is `0`.

### Value

Updated `FourC` object that contains two new `assays` `countsLeftFragmentEnd` and `countsRightFragmentEnd` with the count values at the respective fragment end.

### Author(s)

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

### See Also

`FourC`, `findViewpointFragments`, `countFragmentOverlaps`

### Examples

    ## not run:
    ## countFragmentOverlapsSecondCutter(fc, extend=TRUE, minMapq=30)

[Package FourCSeq version 1.22.1 Index]