Computes eigen vectors for each chromosome using cis contacts and extract chromosome compartments.
getCompartments(
x,
resolution = NULL,
genome = NULL,
chromosomes = NULL,
neigens = 3,
sort_eigens = FALSE,
BPPARAM = BiocParallel::bpparam()
)A HiCExperiment object over a full genome
Which resolution to use to compute eigen vectors
a BSgenome of DNAStringSet object associated with the Hi-C contact matrix.
character or integer vector indicating which
Numver of eigen vectors to extract
Can be FALSE or one of c('Spearman', 'Pearson')
BiocParallel parallelization settings
A HiCExperiment object with additional eigens metadata containing the
normalized eigenvectors and a new "compartments" topologicalFeatures
storing A and B compartments as a GRanges object.
library(HiContacts)
full_contacts_yeast <- contacts_yeast(full = TRUE)
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
comps <- getCompartments(full_contacts_yeast)
#> Going through preflight checklist...
#> Parsing intra-chromosomal contacts for each chromosome...
#> Computing eigenvectors for each chromosome...
metadata(comps)$eigens
#> GRanges object with 763 ranges and 8 metadata columns:
#> seqnames ranges strand | bin_id weight
#> <Rle> <IRanges> <Rle> | <numeric> <numeric>
#> I.I_1_16000 I 1-16000 * | 0 0.0196442
#> I.I_16001_32000 I 16001-32000 * | 1 0.0220746
#> I.I_32001_48000 I 32001-48000 * | 2 0.0188701
#> I.I_48001_64000 I 48001-64000 * | 3 0.0136679
#> I.I_64001_80000 I 64001-80000 * | 4 0.0134860
#> ... ... ... ... . ... ...
#> XVI.XVI_880001_896000 XVI 880001-896000 * | 758 0.00910873
#> XVI.XVI_896001_912000 XVI 896001-912000 * | 759 0.01421350
#> XVI.XVI_912001_928000 XVI 912001-928000 * | 760 0.02439992
#> XVI.XVI_928001_944000 XVI 928001-944000 * | 761 0.01993237
#> XVI.XVI_944001_948066 XVI 944001-948066 * | 762 NaN
#> chr center E1 E2 E3
#> <Rle> <integer> <numeric> <numeric> <numeric>
#> I.I_1_16000 I 8000 0.047017577 -0.373610 0.0785339
#> I.I_16001_32000 I 24000 1.294231824 0.334522 -1.2889302
#> I.I_32001_48000 I 40000 0.111866073 -0.215149 -0.1284306
#> I.I_48001_64000 I 56000 -0.000378168 -0.324072 -0.0859466
#> I.I_64001_80000 I 72000 0.389569315 -0.480918 -0.3674692
#> ... ... ... ... ... ...
#> XVI.XVI_880001_896000 XVI 888000 -0.00143584 0.3904828 0.09137383
#> XVI.XVI_896001_912000 XVI 904000 0.35018650 0.1384289 0.00781169
#> XVI.XVI_912001_928000 XVI 920000 0.99967206 0.1838062 -0.04602689
#> XVI.XVI_928001_944000 XVI 936000 0.83302465 0.0143616 -0.11450504
#> XVI.XVI_944001_948066 XVI 946033 0.00000000 0.0000000 0.00000000
#> eigen
#> <numeric>
#> I.I_1_16000 0.047017577
#> I.I_16001_32000 1.294231824
#> I.I_32001_48000 0.111866073
#> I.I_48001_64000 -0.000378168
#> I.I_64001_80000 0.389569315
#> ... ...
#> XVI.XVI_880001_896000 -0.00143584
#> XVI.XVI_896001_912000 0.35018650
#> XVI.XVI_912001_928000 0.99967206
#> XVI.XVI_928001_944000 0.83302465
#> XVI.XVI_944001_948066 0.00000000
#> -------
#> seqinfo: 16 sequences from an unspecified genome