addViewpointFrags: Add the information of the viewpoint fragments
In FourCSeq: Package analyse 4C sequencing data

Description Usage Arguments Value Author(s) See Also Examples

addViewpointFrags adds the genomic position and information of the viewpoint primer fragments to colData of the FourC object.

1	addViewpointFrags(object, primerFragFile)

`object`	A `FourC` object.
`primerFragFile`	character string defining the file that contains the information about the primer fragments. Defaults to `"primerFragments.rda"` which is the default output file of `findViewpointFragments` in the provided `fragmentDir`.

Updated FourC object with information about the viewpoint fragments added to colData.

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

FourC, findViewpointFragments

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