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rGMAP
September 6, 2018
Type Package
Title Call hierarchical chromatin domains from HiC matrix by GMAP
Version 1.3.1
Date 08-23-2018
Author Wenbao Yu
Maintainer Wenbao Yu 
Description Call hierarchical chromatin domains from HiC contact map by Gaussian Mixture model And Proportion test
BugReports https://github.com/wbaopaul/rGMAP/issues
License GPL (>= 2)
LazyData TRUE
Imports data.table,
ggplot2,
mclust,
EMD,
caTools,
Matrix,
Rcpp (>= 0.12.5)
LinkingTo Rcpp
RoxygenNote 6.1.0
Suggests knitr,
rmarkdown
VignetteBuilder knitr

R topics documented:
data_simu . . . . . . .
hic_rao_IMR90_chr15
plotdom . . . . . . . .
rGMAP . . . . . . . .

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2
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6

1

2

hic_rao_IMR90_chr15

generate simulated hic_mat and true tads

data_simu

Description
generate simulated hic_mat and true tads
Usage
data_simu(stype = "poisson-dist", nratio = 2.5, mu0 = 200,
resl = 1)
Arguments
stype

One of four types of simulated data in the manuscript: poission-dist, poissiondist-hier, nb-dist, nb-dist-hier; poission- or nb- indicates poission distribution or
negative bionomial distribution -hier indicated subtads are generated nestly

nratio

The effect size between intra- and inter domain, larger means higher intra-tad
contacts

mu0

The mean parameter, default 200

resl

Resolution, default set to 1

Value
A list includes following elements:
hic_mat

n by n contact matrix

hierTads

True heirarchical domains

tads_true

True TADs

hic_rao_IMR90_chr15
Normalized Hi-C data for IMR90, chr15 with resolution 10kb.

Description
Normalized Hi-C data for IMR90, chr15 with resolution 10kb.
Usage
hic_rao_IMR90_chr15
Format
A data table with 3 variables:
n1 bin 1
n2 bin 2
count normalized counts

plotdom

3

Source
Rao et al., Cell 2014, A 3D map of the human genome at kilobase resolution reveals principles of
chromatin looping

plotdom

visualize hierarchical domains

Description
visualize hierarchical domains
Usage
plotdom(hic_dat, hiertads_gmap, start_bin, end_bin, cthr = 20,
resl = 10000)
Arguments
hic contact matrix for a given chromosome, either a n by n matrix, or a 3 columns
data.frame   
hiertads_gmap
the hierarchical domains called by GMAP
hic_dat

start_bin

the start bin of the genome

end_bin

the end bin of the genome

cthr

the upper bound count threshold for color, default 20

resl

reslution of Hi-C data, default 10000

rGMAP

Detect hierarchical choromotin domains by GMAP

Description
Detect hierarchical choromotin domains by GMAP
Usage
rGMAP(hic_mat, index_file = NULL, resl = 10 * 10^3, logt = T,
dom_order = 2, maxDistInBin = min(200, 2 * 10^6/resl), min_d = 25,
max_d = 100, min_dp = 5, max_dp = 10, hthr = 0.95, t1thr = 0.5)

4

rGMAP

Arguments
hic_mat

• For single chromosome, supports three types of format:
– a 3-column Hi-C contact matrix, with columns the i_th, j_th bin of a
chromosom and the corresponding contact number
– a n by n matrix, with th element corresponding to contact number
between the i_th and j_th bin of the chromosome
– a text file of the above two types of data
• For multiple chromosomes, a index_file indicates genomic coordinate for
each hic bin should be provided

index_file

A 4-columns tab/space delimited text file indicates the genomic coordinates for
each bin (compatible with HiC-Pro); with columns bin_chr bin_start bin_end
bin_id

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

Value
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

Examples
## 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

rGMAP

5

hic_rao_IMR90_chr15
# normalized Hi-C data for IMR90, chr15 with resolution 10kb
res = rGMAP(hic_rao_IMR90_chr15, resl = 10 * 1000, dom_order = 2)
names(res)
#quickly visualize some hierarchical domains
pp = plotdom(hic_rao_IMR90_chr15, res$hierTads, 6000, 7000, 30, 10)
pp$p2

Index
∗Topic datasets
hic_rao_IMR90_chr15, 2
data_simu, 2
hic_rao_IMR90_chr15, 2
plotdom, 3
rGMAP, 3

6
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