Analyzing Replicated ChIP Sequencing Data Using Quasi-Likelihood


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Documentation for package ‘BinQuasi’ version 0.1-6

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BinQuasi Analyzing Replicated ChIP Sequencing Data Using Quasi-Likelihood
BQ Call peaks in replicated ChIP-seq data using BinQuasi
call.peaks Call peaks from a list of window-level p-values
coef.glm Extract model coefficients
count.table Create a matrix of ChIP-seq count data
NBDev Fit a negative binomial GLM for a given design matrix
PoisDev Compute Poisson deviances for a given design matrix
QL.fit Fit quasi-likelihood models to replicated ChIP-seq data partitioned into a count matrix
QL.results Obtain p- and q-values using results from 'QL.fit'