intervalVars

Given a matrix of normalized signal intensities and the inverse of the
corresponding structure matrices, <code>intervalVars</code> returns the sample
variance of signal intensities of each genomic interval.

Chromatin immunoprecipitation followed by high-throughput
sequencing (ChIP-seq) is the premier technology for profiling genome-wide
localization of chromatin-binding proteins, including transcription
factors and histones with various modifications.
This package provides a robust method for normalizing ChIP-seq
signals across individual samples or groups of samples. It also designs
a self-contained system of statistical models for calling differential
ChIP-seq signals between two or more biological conditions as well as
for calling hypervariable ChIP-seq signals across samples. Refer to
Tu et al. (2021) <doi:10.1101/gr.262675.120> and
Chen et al. (2022) <doi:10.1186/s13059-022-02627-9>
for associated statistical details.

Shiqi Tu

MAnorm2

Tools for Normalizing and Comparing ChIP-seq Samples

intervalVars function

<dl><dt>x</dt>
<dd>A matrix of normalized signal intensities, where each row
represents an interval and each column a sample.</dd>
<dt>inv.strMatrix</dt>
<dd>A list of inversed structure matrices corresponding
to the intervals. Elements of it are recycled if necessary.</dd></dl>

Arguments

Sample Variance of Replicated Signal Intensities — intervalVars

<dl>

<dt>x</dt>
<dd>A matrix of normalized signal intensities, where each row
represents an interval and each column a sample.</dd>


<dt>inv.strMatrix</dt>
<dd>A list of inversed structure matrices corresponding
to the intervals. Elements of it are recycled if necessary.</dd>

</dl>

intervalVars: Sample Variance of Replicated Signal Intensities

Description

Usage

Value

Arguments

See Also