findViewpointFragments {FourCSeq} | R Documentation |
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
findViewpointFragments(object)
object |
A |
Felix A. Klein, felix.klein@embl.de
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