countFragmentOverlaps {FourCSeq} | R Documentation |
countFragmentOverlaps
counts the number of reads mapping to each
fragment end in rowRanges
of the FourC
object.
countFragmentOverlaps(object, trim=0, minMapq=0, shift=0)
object |
A |
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 |
minMapq |
Minimum mapping quality required for counting the read.
Default is |
shift |
Maximum difference in starts or ends between read and fragment
positions. Default is |
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