Description Usage Arguments Value Examples
Detect hierarchical choromotin domains by GMAP
1 2 3 |
hic_obj |
HiC contact matrix, generally either a 3-column data frame/data table or a tab/space delimited text file, corresponding to the i_th, j_th bin of a chromosome and the contact frequency
|
index_obj |
A 4-columns tab/space delimited text file (or corresponding data frame/data table) indicates the genomic coordinates for each bin (compatible with HiC-Pro); with columns bin_chr bin_start bin_end bin_id, default NULL; when index _obj was given, it should be consitent with hic_obj |
resl |
The resolution (bin size), default 10kb |
logt |
Do log-transformation or not, default TRUE |
dom_order |
Maximum level of hierarchical structures, default 2 (call TADs and subTADs) |
maxDistInBin |
Only consider contact whose distance is not greater than maxDistInBIn bins, default 200 bins (or 2Mb) |
min_d |
The minimum d (d: window size), default 25 |
max_d |
The maximum d (d: window size), default 100 |
min_dp |
The minmum dp (dp: lower bound of tad size), defalt 5 |
max_dp |
The maximum dp (dp: lower bound of tad size), defalt 10. min_d, max_d, min_dp and max_dp should be specified in number of bins |
hthr |
The lower bound cutoff for posterior probability, default 0.95 |
t1thr |
Lower bound for t1 for calling TAD, default 0.5 quantile of test statistics of TADs, 0.9 of subTADs |
A list includes following elements:
tads |
A data frame with columns start, end indicates the start and end coordinates of each domain, respectively |
hierTads |
A data frame with columns start, end, dom_order, where dom_order indicates the hierarchical status of a domain, 1 indicates tads, 2 indicates subtads, and so on |
params |
A data frame gives the final parameters for calling TADs |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## On simulated data:
library(rGMAP)
simu_res = data_simu('poisson-dist-hier')
true_domains = simu_res$hierTads
simu_mat = simu_res$hic_mat
predicted_domains = rGMAP(simu_mat, resl = 1)$hierTads
true_domains
predicted_domains
## On an real data example
hic_rao_IMR90_chr15 # normalized Hi-C data for IMR90, chr15 with resolution 10kb
res = rGMAP(hic_rao_IMR90_chr15, NULL, resl = 10 * 1000, dom_order = 2)
names(res)
#quickly visualize some hierarchical domains
pp = plotdom(hic_rao_IMR90_chr15, NULL, res$hierTads, NULL, 6000, 7000, 30, 10)
pp$p2
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.