hic2mat: extract HiC data from .hic file and convert it to squared HiC...
In qunhualilab/hicrep: Measuring the reproducibility of Hi-C data
Description
Usage
Arguments
Value
References
Description
extract HiC data from .hic file and convert it to squared HiC matrix
Usage
1
2
Arguments
file
the path to the .hic file.
chromosome1
character number which specify chromosome to extract.
chromosome2
for intra-chromosome data, set it same as chromosome 1;
for inter-chromosome, set to another chromosome.
resol
resolution, i.e., bin size.
method
specifies what data to extract, raw or normalized.
Must be one of "NONE", "VC", "VC_SQRT", "KR". "NONE" will gives raw counts.
VC is vanilla coverage, VC_SQRT is square root of vanilla coverage, and KR
is Knight-Ruiz or Balanced normalization.
Value
a squared HiC matrix that can be recongnized by get.scc.
References
HiCRep: assessing the reproducibility of Hi-C data using a
stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip
Gurkan Yardimci, Fan Song, Ross C Hardison, William Stafford Noble,
Feng Yue, Qunhua Li. Genome Research 2017. doi: 10.1101/gr.220640.117
qunhualilab/hicrep documentation built on Feb. 27, 2020, 9:17 p.m.
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Description Usage Arguments Value References
Description
extract HiC data from .hic file and convert it to squared HiC matrix
Usage
1 2 |
Arguments
file |
the path to the .hic file. |
chromosome1 |
character number which specify chromosome to extract. |
chromosome2 |
for intra-chromosome data, set it same as chromosome 1; for inter-chromosome, set to another chromosome. |
resol |
resolution, i.e., bin size. |
method |
specifies what data to extract, raw or normalized. Must be one of "NONE", "VC", "VC_SQRT", "KR". "NONE" will gives raw counts. VC is vanilla coverage, VC_SQRT is square root of vanilla coverage, and KR is Knight-Ruiz or Balanced normalization. |
Value
a squared HiC matrix that can be recongnized by get.scc.
References
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Fan Song, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. Genome Research 2017. doi: 10.1101/gr.220640.117
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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