ChIPComp: Perform hypothesis testing to detect differential binding...
In ChIPComp: Quantitative comparison of multiple ChIP-seq datasets
Description
Usage
Arguments
Value
Author(s)
Examples
Description
Perform hypothesis testing to detect differential binding sites
Usage
1
ChIPComp(countSet,A,threshold=1)
Arguments
countSet
A ChIPComp object.
A
User-specified regions to fit the model.
It is a bed file with three columns, named ("chr","start","end"),
could be separated by space or tab.
threshold
User specified posterior probability threshold. Default is 1.
Value
A object ChIPComp contains
Column chr,start,end are the binding site genomic coordinate;
Column ip_c(\#condition)_r(\#replicate) indicates ChIP counts in \#replicate in \#condition;
Column ct_c(\#condition)_r(\#replicate) indicates smoothing control counts in \#replicate in \#condition;
Column commonPeak 1s indicate common binding sites;
Column prob.post is the posterior probability for each binding site.
Column pvalue.wald is the pvalue of wald test for each binding site.
Author(s)
Hao Wu<hao.wu@emory.edu>, Li Chen <li.chen@emory.edu>
Examples
1
2
ChIPComp documentation built on Nov. 8, 2020, 5:24 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
Perform hypothesis testing to detect differential binding sites
Usage
1 | ChIPComp(countSet,A,threshold=1)
|
Arguments
countSet |
A |
A |
User-specified regions to fit the model. It is a bed file with three columns, named ("chr","start","end"), could be separated by space or tab. |
threshold |
User specified posterior probability threshold. Default is 1. |
Value
A object ChIPComp contains
Column chr,start,end are the binding site genomic coordinate;
Column ip_c(\#condition)_r(\#replicate) indicates ChIP counts in \#replicate in \#condition;
Column ct_c(\#condition)_r(\#replicate) indicates smoothing control counts in \#replicate in \#condition;
Column commonPeak 1s indicate common binding sites;
Column prob.post is the posterior probability for each binding site.
Column pvalue.wald is the pvalue of wald test for each binding site.
Author(s)
Hao Wu<hao.wu@emory.edu>, Li Chen <li.chen@emory.edu>
Examples
1 2 |
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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