intervalVars: Sample Variance of Replicated Signal Intensities

In MAnorm2: Tools for Normalizing and Comparing ChIP-seq Samples

Sample Variance of Replicated Signal Intensities

Description

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

Usage

intervalVars(x, inv.strMatrix)

Arguments

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

Value

A numeric vector of the sample variances.

Note

For the ith interval, ti * Si is the covariance matrix of the signal intensities of the interval, where ti is a scalar quantifying the variation level of these signal intensities (under this biological condition), and Si is the interval's structure matrix (under this biological condition). intervalVars returns exactly the sample estimate of each ti.

See Also

bioCond for creating an R object representing a biological condition, and setWeight for modifying the structure matrices of such an object.

MAnorm2 documentation built on Oct. 29, 2022, 1:12 a.m.