Description Usage Arguments Details Value Examples
Reads pairwise ChIA-PET interaction from an input file.
1 | parseLoopsTang(inFile, ...)
|
inFile |
input file with loops |
... |
additional arguments, that will be passed to
|
It reads files with the following tab-delimited format:
chr12 | 48160351 | 48161634 | chr12 | 48230665 | 48232848 | 27 |
chr7 | 77284664 | 77285815 | chr7 | 77388242 | 77388928 | 7 |
chr4 | 128459961 | 128460166 | chr4 | 128508304 | 128509082 | 4 |
This file format was used for ChIA-PET interaction data by Tang et al. 2015 http://dx.doi.org/10.1016/j.cell.2015.11.024. The last column of input file is added as annotation column with colname "score".
An GInteractions
with loops from input file.
1 2 3 4 5 6 7 8 9 10 11 | exampleLoopTang2015File <- system.file("extdata",
"ChIA-PET_GM12878_Tang2015.chr22_1-30000000.clusters.txt",
package = "sevenC")
gi <- parseLoopsTang(exampleLoopTang2015File)
# read loops with custom seqinfo object:
customSeqInfo <- Seqinfo(seqnames = c("chr1", "chr22"),
seqlengths = c(10^8, 10^8), isCircular = c(FALSE, FALSE),
genome = "custom")
gi <- parseLoopsTang(exampleLoopTang2015File, seqinfo = customSeqInfo)
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