FourCSeq (version 1.6.2)

addFragments: Add the restriction fragment information

Description

addFragments adds the genomic position and information of the restriction fragments as GRanges object to rowRanges of the FourC object.

Usage

addFragments(object, minSize = 20, filter = TRUE, save = FALSE)

Arguments

object

A FourC object.

minSize

Minimum size of a restriction fragment end to be valid. Default is 20 bases.

filter

Defines whether fragments that do not contain a cutting site of the second restriction enzyme or are smaller than minSize should be filtered out.

save

Defines if the fragment information should be saved as txt and bed files in the fragmentDir folder of the projectPath.

Value

Updated FourC object that contains the information about the restriction fragments in rowRanges.

See Also

FourC, findViewpointFragments

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)
fc