countFragmentOverlaps: Count fragment overlaps
In FourCSeq: Package analyse 4C sequencing data

Description Usage Arguments Value Author(s) See Also Examples

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

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

`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`.

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

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

FourC, findViewpointFragments, countFragmentOverlapsSecondCutter

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