| addFragments {FourCSeq} | R Documentation |
addFragments adds the genomic position and information of the
restriction fragments as GRanges object to rowRanges of
the FourC object.
addFragments(object, minSize = 20, filter = TRUE, save = FALSE)
object |
A |
minSize |
Minimum size of a restriction fragment end to be valid.
Default is |
filter |
Defines whether fragments that do not contain a cutting site
of the second restriction enzyme or are smaller than |
save |
Defines if the fragment information should be saved as txt and bed files in the fragmentDir folder of the projectPath. |
Updated FourC object that contains the information about
the restriction fragments in rowRanges.
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)
fc