countFragmentOverlaps {FourCSeq} | R Documentation

## Count fragment overlaps

### Description

`countFragmentOverlaps` counts the number of reads mapping to each fragment end in `rowRanges` of the `FourC` object.

### Usage

    countFragmentOverlaps(object, trim=0, minMapq=0, shift=0)

### Arguments

`object` | A `FourC` object.
`trim` | Number of bases that should be trimmed at the start of a read. This is necessary if the read still contains the restriction enzyme sequence. Default is `0` bases.
`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`, `countFragmentOverlapsSecondCutter`

### Examples

    metadata <- list(projectPath=tempdir(),
                     fragmentDir="re_fragments",
                     referenceGenomeFile=system.file("extdata/dm3_chr2L_1-6900.fa",
                                                     package="FourCSeq"),
                     reSequence1="GATC",
                     reSequence2="CATG",
                     primerFile=system.file("extdata/primer.fa",
                                            package="FourCSeq"),
                     bamFilePath=system.file("extdata/bam", package="FourCSeq"))

    colData <- DataFrame(viewpoint = "testdata",
                         condition = factor(rep(c("WE_68h", "MESO_68h", "WE_34h"),
                                                each=2),
                                            levels = c("WE_68h", "MESO_68h", "WE_34h")),
                         replicate = rep(c(1, 2),
                                         3),
                         bamFile = c("CRM_ap_ApME680_WE_6-8h_1_testdata.bam",
                                     "CRM_ap_ApME680_WE_6-8h_2_testdata.bam",
                                     "CRM_ap_ApME680_MESO_6-8h_1_testdata.bam",
                                     "CRM_ap_ApME680_MESO_6-8h_2_testdata.bam",
                                     "CRM_ap_ApME680_WE_3-4h_1_testdata.bam",
                                     "CRM_ap_ApME680_WE_3-4h_2_testdata.bam"),
                         sequencingPrimer="first")

    fc <- FourC(colData, metadata)
    fc

    fc <- addFragments(fc)

    findViewpointFragments(fc)

    fc <- addViewpointFrags(fc)
    fc

    fc <- countFragmentOverlaps(fc, trim=4, minMapq=30)
    fc

[Package FourCSeq version 1.21.0 Index]