From a (m)cool pre-imported in memory, computes a 4C profile
using a user-specified viewpoint.
virtual4C(x, viewpoint, use.scores = "balanced")a HiCExperiment object
viewpoint, defined as a GRanges
use.scores
A tibble with the contact frequency of the viewpoint, per bin along the imported genomic range.
library(HiContacts)
contacts_yeast <- contacts_yeast()
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
v4C <- virtual4C(contacts_yeast, GenomicRanges::GRanges('II:490001-510000'))
v4C
#> GRanges object with 763 ranges and 4 metadata columns:
#> seqnames ranges strand | score center in_viewpoint
#> <Rle> <IRanges> <Rle> | <numeric> <numeric> <logical>
#> [1] I 1-16000 * | 0.00359351 8000.5 FALSE
#> [2] I 16001-32000 * | 0.00222557 24000.5 FALSE
#> [3] I 32001-48000 * | 0.00422662 40000.5 FALSE
#> [4] I 48001-64000 * | 0.00248154 56000.5 FALSE
#> [5] I 64001-80000 * | 0.00260842 72000.5 FALSE
#> ... ... ... ... . ... ... ...
#> [759] XVI 880001-896000 * | 0.00301663 888000 FALSE
#> [760] XVI 896001-912000 * | 0.00397464 904000 FALSE
#> [761] XVI 912001-928000 * | 0.00546521 920000 FALSE
#> [762] XVI 928001-944000 * | 0.00501920 936000 FALSE
#> [763] XVI 944001-948066 * | 0.00000000 946034 FALSE
#> viewpoint
#> <character>
#> [1] II:490001-510000
#> [2] II:490001-510000
#> [3] II:490001-510000
#> [4] II:490001-510000
#> [5] II:490001-510000
#> ... ...
#> [759] II:490001-510000
#> [760] II:490001-510000
#> [761] II:490001-510000
#> [762] II:490001-510000
#> [763] II:490001-510000
#> -------
#> seqinfo: 16 sequences from an unspecified genome; no seqlengths