Expand description
edgeR glmFit + glmLRT: negative-binomial GLM fit and likelihood-ratio test of a coefficient or contrast. Method: McCarthy, Chen & Smyth (2012), NAR 40:4288-4297. Per gene the full design is fit by NB IRLS (log link), the LR statistic is the drop in NB deviance from the reduced model, and its p-value is the chi-square upper tail on the tested degrees of freedom. logFC is the tested coefficient/contrast from edgeR’s predFC (prior.count 0.125 shrinkage) rescaled to log2; logCPM is aveLogCPM (prior.count 2, dispersion 0.05).
Structs§
- Design
- Design matrix: row-major n_samples × n_coef, plus column names from the header.
- GlmLrt
Args - Matrix