HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides a R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms.
License: Other
I recently used HiCBricks and I just wonder, is there any way to get the Pearson correlation matrix, which is the middle product in the Brick_call_compartments() ?
Several questions need to be answered before I can do this. The biggest one being, how do I get a HiCExplorer file?
A potential problem here. When x_coords and y_coords are not the same, y_axis inherits axis labels and values from x_axis. Refer, line 222 - 235 in Brick_vizart_plot_heatmap.
Or at least enable choose "cis" ones?
Hi,
I would like to generate plots using HiCBricks to generate HiC plots for publications.
I run into troubles when loading data:
cool_file1 <- "/home/momi/hg-tmp/DpnII_alto_salmon_unphased.matrix.mcool"
out_dir <- file.path("/home/momi/hg-tmp/","mcool_to_Brick_test")
dir.create(out_dir)
Create_many_Bricks_from_mcool(output_directory = out_dir,
file_prefix = "mcool_to_Brick_test",
mcool = cool_file1,
resolution = 10000,
experiment_name = "Testing mcool creation",
remove_existing = TRUE)
I get the following error which was mentioned in another issue as well but i couldnt figure out if it was resolved.
Create_many_Bricks_from_mcool(output_directory = out_dir,
+ file_prefix = "mcool_to_Brick_test",
+ mcool = cool_file1,
+ resolution = 10000,
+ experiment_name = "Testing mcool creation",
+ remove_existing = TRUE)
Provided mcool is a version 3 file.
Error in rep(chr, Offset) : invalid 'times' argument
Any hints would be appreciated.
Thank you,
Michel
file info:
> h5ls(cool_file1)
group name otype dclass dim
0 / resolutions H5I_GROUP
1 /resolutions 1000 H5I_GROUP
2 /resolutions/1000 bins H5I_GROUP
3 /resolutions/1000/bins chrom H5I_DATASET INTEGER 2758598
4 /resolutions/1000/bins end H5I_DATASET INTEGER 2758598
5 /resolutions/1000/bins start H5I_DATASET INTEGER 2758598
6 /resolutions/1000 chroms H5I_GROUP
7 /resolutions/1000/chroms length H5I_DATASET INTEGER 4011
8 /resolutions/1000/chroms name H5I_DATASET STRING 4011
9 /resolutions/1000 indexes H5I_GROUP
10 /resolutions/1000/indexes bin1_offset H5I_DATASET INTEGER 2758599
11 /resolutions/1000/indexes chrom_offset H5I_DATASET INTEGER 4012
12 /resolutions/1000 pixels H5I_GROUP
13 /resolutions/1000/pixels bin1_id H5I_DATASET INTEGER 25660039
14 /resolutions/1000/pixels bin2_id H5I_DATASET INTEGER 25660039
15 /resolutions/1000/pixels count H5I_DATASET INTEGER 25660039
16 /resolutions 10000 H5I_GROUP
17 /resolutions/10000 bins H5I_GROUP
18 /resolutions/10000/bins chrom H5I_DATASET INTEGER 277638
19 /resolutions/10000/bins end H5I_DATASET INTEGER 277638
20 /resolutions/10000/bins start H5I_DATASET INTEGER 277638
21 /resolutions/10000 chroms H5I_GROUP
22 /resolutions/10000/chroms length H5I_DATASET INTEGER 4011
23 /resolutions/10000/chroms name H5I_DATASET STRING 4011
24 /resolutions/10000 indexes H5I_GROUP
25 /resolutions/10000/indexes bin1_offset H5I_DATASET INTEGER 277639
26 /resolutions/10000/indexes chrom_offset H5I_DATASET INTEGER 4012
27 /resolutions/10000 pixels H5I_GROUP
28 /resolutions/10000/pixels bin1_id H5I_DATASET INTEGER 22843881
29 /resolutions/10000/pixels bin2_id H5I_DATASET INTEGER 22843881
30 /resolutions/10000/pixels count H5I_DATASET INTEGER 22843881
31 /resolutions 100000 H5I_GROUP
32 /resolutions/100000 bins H5I_GROUP
33 /resolutions/100000/bins chrom H5I_DATASET INTEGER 30317
34 /resolutions/100000/bins end H5I_DATASET INTEGER 30317
35 /resolutions/100000/bins start H5I_DATASET INTEGER 30317
36 /resolutions/100000 chroms H5I_GROUP
37 /resolutions/100000/chroms length H5I_DATASET INTEGER 4011
38 /resolutions/100000/chroms name H5I_DATASET STRING 4011
39 /resolutions/100000 indexes H5I_GROUP
40 /resolutions/100000/indexes bin1_offset H5I_DATASET INTEGER 30318
41 /resolutions/100000/indexes chrom_offset H5I_DATASET INTEGER 4012
42 /resolutions/100000 pixels H5I_GROUP
43 /resolutions/100000/pixels bin1_id H5I_DATASET INTEGER 15220297
44 /resolutions/100000/pixels bin2_id H5I_DATASET INTEGER 15220297
45 /resolutions/100000/pixels count H5I_DATASET INTEGER 15220297
46 /resolutions 1000000 H5I_GROUP
47 /resolutions/1000000 bins H5I_GROUP
48 /resolutions/1000000/bins chrom H5I_DATASET INTEGER 6501
49 /resolutions/1000000/bins end H5I_DATASET INTEGER 6501
50 /resolutions/1000000/bins start H5I_DATASET INTEGER 6501
51 /resolutions/1000000 chroms H5I_GROUP
52 /resolutions/1000000/chroms length H5I_DATASET INTEGER 4011
53 /resolutions/1000000/chroms name H5I_DATASET STRING 4011
54 /resolutions/1000000 indexes H5I_GROUP
55 /resolutions/1000000/indexes bin1_offset H5I_DATASET INTEGER 6502
56 /resolutions/1000000/indexes chrom_offset H5I_DATASET INTEGER 4012
57 /resolutions/1000000 pixels H5I_GROUP
58 /resolutions/1000000/pixels bin1_id H5I_DATASET INTEGER 3496226
59 /resolutions/1000000/pixels bin2_id H5I_DATASET INTEGER 3496226
60 /resolutions/1000000/pixels count H5I_DATASET INTEGER 3496226
61 /resolutions 10000000 H5I_GROUP
62 /resolutions/10000000 bins H5I_GROUP
63 /resolutions/10000000/bins chrom H5I_DATASET INTEGER 4247
64 /resolutions/10000000/bins end H5I_DATASET INTEGER 4247
65 /resolutions/10000000/bins start H5I_DATASET INTEGER 4247
66 /resolutions/10000000 chroms H5I_GROUP
67 /resolutions/10000000/chroms length H5I_DATASET INTEGER 4011
68 /resolutions/10000000/chroms name H5I_DATASET STRING 4011
69 /resolutions/10000000 indexes H5I_GROUP
70 /resolutions/10000000/indexes bin1_offset H5I_DATASET INTEGER 4248
71 /resolutions/10000000/indexes chrom_offset H5I_DATASET INTEGER 4012
72 /resolutions/10000000 pixels H5I_GROUP
73 /resolutions/10000000/pixels bin1_id H5I_DATASET INTEGER 352286
74 /resolutions/10000000/pixels bin2_id H5I_DATASET INTEGER 352286
75 /resolutions/10000000/pixels count H5I_DATASET INTEGER 352286
76 /resolutions 2000 H5I_GROUP
77 /resolutions/2000 bins H5I_GROUP
78 /resolutions/2000/bins chrom H5I_DATASET INTEGER 1380287
79 /resolutions/2000/bins end H5I_DATASET INTEGER 1380287
80 /resolutions/2000/bins start H5I_DATASET INTEGER 1380287
81 /resolutions/2000 chroms H5I_GROUP
82 /resolutions/2000/chroms length H5I_DATASET INTEGER 4011
83 /resolutions/2000/chroms name H5I_DATASET STRING 4011
84 /resolutions/2000 indexes H5I_GROUP
85 /resolutions/2000/indexes bin1_offset H5I_DATASET INTEGER 1380288
86 /resolutions/2000/indexes chrom_offset H5I_DATASET INTEGER 4012
87 /resolutions/2000 pixels H5I_GROUP
88 /resolutions/2000/pixels bin1_id H5I_DATASET INTEGER 25269260
89 /resolutions/2000/pixels bin2_id H5I_DATASET INTEGER 25269260
90 /resolutions/2000/pixels count H5I_DATASET INTEGER 25269260
91 /resolutions 25000 H5I_GROUP
92 /resolutions/25000 bins H5I_GROUP
93 /resolutions/25000/bins chrom H5I_DATASET INTEGER 112365
94 /resolutions/25000/bins end H5I_DATASET INTEGER 112365
95 /resolutions/25000/bins start H5I_DATASET INTEGER 112365
96 /resolutions/25000 chroms H5I_GROUP
97 /resolutions/25000/chroms length H5I_DATASET INTEGER 4011
98 /resolutions/25000/chroms name H5I_DATASET STRING 4011
99 /resolutions/25000 indexes H5I_GROUP
100 /resolutions/25000/indexes bin1_offset H5I_DATASET INTEGER 112366
101 /resolutions/25000/indexes chrom_offset H5I_DATASET INTEGER 4012
102 /resolutions/25000 pixels H5I_GROUP
103 /resolutions/25000/pixels bin1_id H5I_DATASET INTEGER 20285503
104 /resolutions/25000/pixels bin2_id H5I_DATASET INTEGER 20285503
105 /resolutions/25000/pixels count H5I_DATASET INTEGER 20285503
106 /resolutions 250000 H5I_GROUP
107 /resolutions/250000 bins H5I_GROUP
108 /resolutions/250000/bins chrom H5I_DATASET INTEGER 14274
109 /resolutions/250000/bins end H5I_DATASET INTEGER 14274
110 /resolutions/250000/bins start H5I_DATASET INTEGER 14274
111 /resolutions/250000 chroms H5I_GROUP
112 /resolutions/250000/chroms length H5I_DATASET INTEGER 4011
113 /resolutions/250000/chroms name H5I_DATASET STRING 4011
114 /resolutions/250000 indexes H5I_GROUP
115 /resolutions/250000/indexes bin1_offset H5I_DATASET INTEGER 14275
116 /resolutions/250000/indexes chrom_offset H5I_DATASET INTEGER 4012
117 /resolutions/250000 pixels H5I_GROUP
118 /resolutions/250000/pixels bin1_id H5I_DATASET INTEGER 10900994
119 /resolutions/250000/pixels bin2_id H5I_DATASET INTEGER 10900994
120 /resolutions/250000/pixels count H5I_DATASET INTEGER 10900994
121 /resolutions 2500000 H5I_GROUP
122 /resolutions/2500000 bins H5I_GROUP
123 /resolutions/2500000/bins chrom H5I_DATASET INTEGER 4995
124 /resolutions/2500000/bins end H5I_DATASET INTEGER 4995
125 /resolutions/2500000/bins start H5I_DATASET INTEGER 4995
126 /resolutions/2500000 chroms H5I_GROUP
127 /resolutions/2500000/chroms length H5I_DATASET INTEGER 4011
128 /resolutions/2500000/chroms name H5I_DATASET STRING 4011
129 /resolutions/2500000 indexes H5I_GROUP
130 /resolutions/2500000/indexes bin1_offset H5I_DATASET INTEGER 4996
131 /resolutions/2500000/indexes chrom_offset H5I_DATASET INTEGER 4012
132 /resolutions/2500000 pixels H5I_GROUP
133 /resolutions/2500000/pixels bin1_id H5I_DATASET INTEGER 1048644
134 /resolutions/2500000/pixels bin2_id H5I_DATASET INTEGER 1048644
135 /resolutions/2500000/pixels count H5I_DATASET INTEGER 1048644
136 /resolutions 5000 H5I_GROUP
137 /resolutions/5000 bins H5I_GROUP
138 /resolutions/5000/bins chrom H5I_DATASET INTEGER 553290
139 /resolutions/5000/bins end H5I_DATASET INTEGER 553290
140 /resolutions/5000/bins start H5I_DATASET INTEGER 553290
141 /resolutions/5000 chroms H5I_GROUP
142 /resolutions/5000/chroms length H5I_DATASET INTEGER 4011
143 /resolutions/5000/chroms name H5I_DATASET STRING 4011
144 /resolutions/5000 indexes H5I_GROUP
145 /resolutions/5000/indexes bin1_offset H5I_DATASET INTEGER 553291
146 /resolutions/5000/indexes chrom_offset H5I_DATASET INTEGER 4012
147 /resolutions/5000 pixels H5I_GROUP
148 /resolutions/5000/pixels bin1_id H5I_DATASET INTEGER 24215756
149 /resolutions/5000/pixels bin2_id H5I_DATASET INTEGER 24215756
150 /resolutions/5000/pixels count H5I_DATASET INTEGER 24215756
151 /resolutions 50000 H5I_GROUP
152 /resolutions/50000 bins H5I_GROUP
153 /resolutions/50000/bins chrom H5I_DATASET INTEGER 57489
154 /resolutions/50000/bins end H5I_DATASET INTEGER 57489
155 /resolutions/50000/bins start H5I_DATASET INTEGER 57489
156 /resolutions/50000 chroms H5I_GROUP
157 /resolutions/50000/chroms length H5I_DATASET INTEGER 4011
158 /resolutions/50000/chroms name H5I_DATASET STRING 4011
159 /resolutions/50000 indexes H5I_GROUP
160 /resolutions/50000/indexes bin1_offset H5I_DATASET INTEGER 57490
161 /resolutions/50000/indexes chrom_offset H5I_DATASET INTEGER 4012
162 /resolutions/50000 pixels H5I_GROUP
163 /resolutions/50000/pixels bin1_id H5I_DATASET INTEGER 17955214
164 /resolutions/50000/pixels bin2_id H5I_DATASET INTEGER 17955214
165 /resolutions/50000/pixels count H5I_DATASET INTEGER 17955214
166 /resolutions 500000 H5I_GROUP
167 /resolutions/500000 bins H5I_GROUP
168 /resolutions/500000/bins chrom H5I_DATASET INTEGER 9049
169 /resolutions/500000/bins end H5I_DATASET INTEGER 9049
170 /resolutions/500000/bins start H5I_DATASET INTEGER 9049
171 /resolutions/500000 chroms H5I_GROUP
172 /resolutions/500000/chroms length H5I_DATASET INTEGER 4011
173 /resolutions/500000/chroms name H5I_DATASET STRING 4011
174 /resolutions/500000 indexes H5I_GROUP
175 /resolutions/500000/indexes bin1_offset H5I_DATASET INTEGER 9050
176 /resolutions/500000/indexes chrom_offset H5I_DATASET INTEGER 4012
177 /resolutions/500000 pixels H5I_GROUP
178 /resolutions/500000/pixels bin1_id H5I_DATASET INTEGER 7263989
179 /resolutions/500000/pixels bin2_id H5I_DATASET INTEGER 7263989
180 /resolutions/500000/pixels count H5I_DATASET INTEGER 7263989
181 /resolutions 5000000 H5I_GROUP
182 /resolutions/5000000 bins H5I_GROUP
183 /resolutions/5000000/bins chrom H5I_DATASET INTEGER 4497
184 /resolutions/5000000/bins end H5I_DATASET INTEGER 4497
185 /resolutions/5000000/bins start H5I_DATASET INTEGER 4497
186 /resolutions/5000000 chroms H5I_GROUP
187 /resolutions/5000000/chroms length H5I_DATASET INTEGER 4011
188 /resolutions/5000000/chroms name H5I_DATASET STRING 4011
189 /resolutions/5000000 indexes H5I_GROUP
190 /resolutions/5000000/indexes bin1_offset H5I_DATASET INTEGER 4498
191 /resolutions/5000000/indexes chrom_offset H5I_DATASET INTEGER 4012
192 /resolutions/5000000 pixels H5I_GROUP
193 /resolutions/5000000/pixels bin1_id H5I_DATASET INTEGER 553438
194 /resolutions/5000000/pixels bin2_id H5I_DATASET INTEGER 553438
195 /resolutions/5000000/pixels count H5I_DATASET INTEGER 553438
Thanks for providing this efficient tool.
I wonder is it possible to plot aggregated Hi-C sub-matrices of a specified list of positions, such as sub-contacts around some histone peaks?
similar function as this one.
https://hicexplorer.readthedocs.io/en/latest/content/tools/hicAggregateContacts.html#hicaggregatecontacts
thank you!
Implement the Brick container class for parallelized workflows and automated data loading.
Found a bug when a CreateBrick command is issued with the args remove.existing = TRUE.
If a previous brick was created but for a variety of reasons it encountered an error and could not be tracked, then in this case when the same brick is recreated the removal of the previous tracking tag will produce an incorrect error with the message "Brick is not being tracked!"
If x_axis is provided as FALSE, then Brick_vizart does not plot y_axis labels. Refer to line 468 in function viz_art_backend > Get_heatmap_theme.
Implement a direct read access for .hic files.
Hi there,
Is there a coordinate syntax for ploting multiple chromosomes at once using Brick_vizart_plot_heatmap? This would be a very useful feature for those of us using HiC data for eukaryotic genome assembly.
Pros:
Cons:
The above procedure seems clunky, and introduces another layer of complexity, so I do not think users will really go for this.
And anyways, how many Hi-C studies are there that do comparisons across normalizations?
Hello,
I have been trying to load an mcool file into HiCBricks, but keep getting the following error:
Error in Brick_load_data_from_mcool(Brick = file_brick, mcool = "file.mcool", :
object 'Norm.factor' not found
Here is what I did:
cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 \
chromsizes:10000 \
file.pairs file.cool
cooler balance -p 12 --mad-max 10 file.cool
cooler zoomify --balance --balance-args '--mad-max 10' file.coolfile_brick = CreateBrick_from_mcool(Brick='file.brick', mcool='file.mcool', binsize=10000)
file_data = Brick_load_data_from_mcool(Brick=file_brick, mcool='file.mcool', chr1='chr1', chr2='chr1', binsize=10000)I tried setting norm.factor to NULL in Brick_load_data_from_mcool, but keep getting the same error.
Do you have an idea why this is happening ?
Here are the attributes of file.mcool::/resolutions/10000:
'@attrs':
bin-size: 10000
bin-type: fixed
creation-date: 2019-05-09 19:52:48.969380
format: HDF5::Cooler
format-url: https://github.com/mirnylab/cooler
format-version: 3
generated-by: cooler-0.8.5
genome-assembly: unknown
metadata: {}
nbins: 313767
nchroms: 95
nnz: 136619590
storage-mode: symmetric-upper
sum: 373921250
bins:
'@attrs': {}
chrom:
'@attrs': {}
end:
'@attrs': {}
start:
'@attrs': {}
weight:
'@attrs': {cis_only: false, converged: true, ignore_diags: 2, mad_max: 10, min_count: 0,
min_nnz: 10, scale: 2275.654791260843, tol: 1.0e-05, var: 9.55998041947331e-06}
chroms:
'@attrs': {}
length:
'@attrs': {}
name:
'@attrs': {}
indexes:
'@attrs': {}
bin1_offset:
'@attrs': {}
chrom_offset:
'@attrs': {}
pixels:
'@attrs': {}
bin1_id:
'@attrs': {}
bin2_id:
'@attrs': {}
count:
'@attrs': {}
I encountered the following issue with running HiCBricks::Create_many_Bricks, following the vignette examples.
Error in h5writeDataset.data.frame(h5loc = Brick.handler, obj = object, :
could not find function "h5writeDataset.data.frame"
As a workaround, the "hdf5r" package needs to be installed from CRAN separately, HiCBricks can then be called without errors and writes to disk.
dir.create(out_dir)
h5writeDataset.data.frame <- rhdf5::h5writeDataset
h5writeDataset.array <- rhdf5::h5writeDataset
Create_many_Bricks(...)
Clearly this is not ideal so if the dependencies can be installed correctly based on the DESCRIPTION and NAMESPACE that would avoid this problem.
I am using R v4.1.2 on a RHEL 8 linux server with the latest versions of packages installed from Bioconductor and CRAN.
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.5 (Ootpa)
Matrix products: default
BLAS: /usr/local/R-4.1.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.1.2/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] hdf5r_1.3.5 HiCBricks_1.11.0 R6_2.5.1 rhdf5_2.38.0 curl_4.3.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.2 purrr_0.3.4 reshape2_1.4.4 colorspace_2.0-3
[5] vctrs_0.3.8 generics_0.1.2 stats4_4.1.2 viridisLite_0.4.0
[9] utf8_1.2.2 rlang_1.0.2 R.oo_1.24.0 pillar_1.7.0
[13] R.utils_2.11.0 glue_1.6.2 DBI_1.1.2 BiocParallel_1.28.3
[17] BiocGenerics_0.40.0 bit64_4.0.5 RColorBrewer_1.1-3 GenomeInfoDbData_1.2.7
[21] lifecycle_1.0.1 plyr_1.8.6 stringr_1.4.0 zlibbioc_1.40.0
[25] munsell_0.5.0 gtable_0.3.0 R.methodsS3_1.8.1 tzdb_0.2.0
[29] IRanges_2.28.0 GenomeInfoDb_1.30.1 parallel_4.1.2 fansi_1.0.2
[33] Rcpp_1.0.8.3 readr_2.1.2 scales_1.1.1 S4Vectors_0.32.3
[37] vroom_1.5.7 jsonlite_1.8.0 XVector_0.34.0 bit_4.0.4
[41] gridExtra_2.3 hms_1.1.1 ggplot2_3.3.5 digest_0.6.29
[45] stringi_1.7.6 dplyr_1.0.8 GenomicRanges_1.46.1 cli_3.2.0
[49] tools_4.1.2 bitops_1.0-7 rhdf5filters_1.6.0 magrittr_2.0.2
[53] RCurl_1.98-1.6 tibble_3.1.6 crayon_1.5.0 pkgconfig_2.0.3
[57] ellipsis_0.3.2 data.table_1.14.2 assertthat_0.2.1 rstudioapi_0.13
[61] viridis_0.6.2 Rhdf5lib_1.16.0 compiler_4.1.2
Hello Koustav,
The next Bioconductor release 3.15 is scheduled for April 27th. Commits to the
current 3.14 release should be made by April 8th and the last day to commit to
the devel branch is April 22nd. We like to make an effort to have all
Bioconductor packages building and checking without ERROR or TIMEOUT in both
release and devel versions. For some reason the email I sent was undeliverable
which is why I'm opening an issue on the GitHub.
Currently your package is producing an ERROR across all builders in the release
version of Bioconductor. Could you please investigate the error as soon as
possible?
Release version -
https://bioconductor.org/checkResults/3.14/bioc-LATEST/HiCBricks/
If you need any assistance please feel free to ask questions at
[email protected].
Thank you,
Kayla
Show me an image of a HiCBricks plot
Hi,
Has anyone come across problems to read the mcool files converted by hicexplorer? Not sure what went wrong, can someone give some hints where should I change in mcool?
Thanks!
First, I figured out there should be "format-version" attribute in mcool file, so I added it back "format-version: 2". (I guess it should be 2. I tried 1 and 3, didn't read either)
However, it threw the following error:
output=CreateBrick_from_mcool(Brick="./test40k", binsize=40000, mcool="Merged.4bins_corrected.mcool", remove.existing=T)
Error in rep(chr, Offset) : invalid 'times' argument
Here I listed the file content, one from my file and the other one from the example:
h5ls("Merged.4bins_corrected.mcool")
group name otype dclass dim
0 / resolutions H5I_GROUP
1 /resolutions 40000 H5I_GROUP
2 /resolutions/40000 bins H5I_GROUP
3 /resolutions/40000/bins chrom H5I_DATASET ENUM 27752
4 /resolutions/40000/bins end H5I_DATASET INTEGER 27752
5 /resolutions/40000/bins start H5I_DATASET INTEGER 27752
6 /resolutions/40000/bins weight H5I_DATASET FLOAT 27752
7 /resolutions/40000 chroms H5I_GROUP
8 /resolutions/40000/chroms length H5I_DATASET INTEGER 32
9 /resolutions/40000/chroms name H5I_DATASET STRING 32
10 /resolutions/40000 indexes H5I_GROUP
11 /resolutions/40000/indexes bin1_offset H5I_DATASET INTEGER 27753
12 /resolutions/40000/indexes chrom_offset H5I_DATASET INTEGER 33
13 /resolutions/40000 pixels H5I_GROUP
14 /resolutions/40000/pixels bin1_id H5I_DATASET INTEGER 81274286
15 /resolutions/40000/pixels bin2_id H5I_DATASET INTEGER 81274286
16 /resolutions/40000/pixels count H5I_DATASET FLOAT 81274286
h5ls("../4DNFI7JNCNFB.mcool")
group name otype dclass dim
0 / resolutions H5I_GROUP
1 /resolutions 1000 H5I_GROUP
2 /resolutions/1000 bins H5I_GROUP
3 /resolutions/1000/bins KR H5I_DATASET FLOAT 3088281
4 /resolutions/1000/bins VC H5I_DATASET FLOAT 3088281
5 /resolutions/1000/bins VC_SQRT H5I_DATASET FLOAT 3088281
6 /resolutions/1000/bins chrom H5I_DATASET ENUM 3088281
7 /resolutions/1000/bins end H5I_DATASET INTEGER 3088281
8 /resolutions/1000/bins start H5I_DATASET INTEGER 3088281
9 /resolutions/1000/bins weight H5I_DATASET FLOAT 3088281
10 /resolutions/1000 chroms H5I_GROUP
11 /resolutions/1000/chroms length H5I_DATASET INTEGER 24
12 /resolutions/1000/chroms name H5I_DATASET STRING 24
13 /resolutions/1000 indexes H5I_GROUP
14 /resolutions/1000/indexes bin1_offset H5I_DATASET INTEGER 3088282
15 /resolutions/1000/indexes chrom_offset H5I_DATASET INTEGER 25
16 /resolutions/1000 pixels H5I_GROUP
17 /resolutions/1000/pixels bin1_id H5I_DATASET INTEGER 356526446
18 /resolutions/1000/pixels bin2_id H5I_DATASET INTEGER 356526446
19 /resolutions/1000/pixels count H5I_DATASET INTEGER 356526446
20 /resolutions 10000 H5I_GROUP
21 /resolutions/10000 bins H5I_GROUP
22 /resolutions/10000/bins KR H5I_DATASET FLOAT 308837
23 /resolutions/10000/bins VC H5I_DATASET FLOAT 308837
Hi,
I installed HiCBricks as BiocManager::install("HiCBricks", version = "3.9") (also, tried the latest version from GitHub). Then, I tried following the vignette. The first command:
Bintable_path <- system.file(file.path("extdata",
"Bintable_100kb.bins"), package = "HiCBricks")
gives empty Bintable_path.
> Bintable_path
[1] ""
OK, one can download the file manually from GitHub Bintable_100kb.bins.
The second command also fails:
> HiCBricks::Create_many_Bricks(BinTable = Bintable_path,
... bin_delim=" ", output_directory = out_dir,
... file_prefix = "HiCBricks_vignette_test", remove_existing=TRUE,
... experiment_name = "HiCBricks vignette test", resolution = 100000)
Error: 'Create_many_Bricks' is not an exported object from 'namespace:HiCBricks'
What may be wrong?
Hi, I'm trying to use HiCBricks (I tried both the GitHub version and the bioconconductor version) with a mcool file converted from juicer using the suggested script (https://github.com/4dn-dcic/hic2cool) which seems to work properly, but I found the following errors:
Output.brick <- CreateBrick_from_mcool(Brick = "/tmp/prova.brick", mcool = "/DATA_NFS/HI-C/monica/juicer_results/132/inter_30.mcool", remove.existing = TRUE)
Can you help me?
Minor Issues:
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