HiCglmi: Probing Factor-Dependent Long-Range Contacts using Regression with Higher-Order Interaction Terms

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We propose a generalized linear regression with higher-order interaction terms to assess the influences of genomic features such as DNA-binding proteins and functional elements on long-range contacts from Hi-C experiments.

Author
Raphael Mourad
Date of publication
2016-10-17 18:59:53
Maintainer
Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>
License
GPL-2
Version
1.0

View on CRAN

Man pages

annotateHiCBin
Annotate Hi-C bins with genomic feature data.
createHiCDataset
Create a dataset for further processing with the R package.
dataExample
Hi-C matrix and ChIP-seq peaks.
filterCouples
Filter Hi-C data based on knowledge.
HiCglmiModel
The generalized linear model with interactions.
HiCglmi-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("HiCglmi")}
HiCglmiProcData
Process data for further generalized linear regression with...
readGFBed
Read genomic feature bed file
testDistancePowerLawDistrib
Check log-log linear relation between distance and Hi-C...

Files in this package

HiCglmi
HiCglmi/inst
HiCglmi/inst/extdata
HiCglmi/inst/extdata/BEAF32_macs2_Kc167_dm3.bed
HiCglmi/NAMESPACE
HiCglmi/data
HiCglmi/data/dataExample.RData
HiCglmi/data/datalist
HiCglmi/R
HiCglmi/R/HiCglmiModel.R
HiCglmi/R/HiCglmiMiscFun.R
HiCglmi/R/HiCglmiProcData.R
HiCglmi/MD5
HiCglmi/build
HiCglmi/build/partial.rdb
HiCglmi/DESCRIPTION
HiCglmi/man
HiCglmi/man/HiCglmiProcData.Rd
HiCglmi/man/HiCglmiModel.Rd
HiCglmi/man/dataExample.Rd
HiCglmi/man/createHiCDataset.Rd
HiCglmi/man/HiCglmi-package.Rd
HiCglmi/man/testDistancePowerLawDistrib.Rd
HiCglmi/man/filterCouples.Rd
HiCglmi/man/readGFBed.Rd
HiCglmi/man/annotateHiCBin.Rd