FourCSeq (version 1.6.2)

findViewpointFragments: Find the fragments to which the viewpoint primers map.

Description

findViewpointFragments finds the position of the viewpoint primer in the reference genome and on which restriction fragment they fall. It saves the results in these files: - projectPath/fragmentDir/primerFragments.rda - projectPath/fragmentDir/primerFragments.txt

Usage

findViewpointFragments(object)

Arguments

object

A FourC object.

See Also

FourC getReferenceSeq

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