DESeq (version 1.24.0)

fitNbinomGLMsForMatrix: Fit negative binomial GLMs to a count matrix.

Description

This is a low-level function that is wrapped by nbinomGLMTest.

Usage

fitNbinomGLMsForMatrix(counts, sizeFactors, rawScv, modelFormula,  modelFrame, quiet = FALSE, reportLog2 = TRUE, glmControl = list() )

Arguments

counts

a matrix of integer counts. Rows for genes, Columns for samples.

sizeFactors

a vector with a size factor for each column in 'counts'.

rawScv

a vector with a raw SCV (i.e., a dispersion) for each row in 'counts'.

modelFormula

a model formula. The left hand side should read 'count ~'.

modelFrame

a model frame (with one row for each column in 'counts')

quiet

whether to not print dots

reportLog2

whether to convert reported coefficients from natural log to log2 scale

glmControl

list of additional parameters to be passed to glm.control

Value

A data frame with one row for each gene and columns as follows:

• one column for each estimated coefficient, on a log2 scale (i.e., the natural log reported by glm is rescaled to base 2)
• a column 'deviance', with the deviance of the fit
• a boolean column 'converged', indicating whether the fit converged

Furthermore, the data frame has a scalar attribute 'df.residual' that contains the number of residual degrees of freedom.

Examples

# See the code of fitNbinomGLMs for an example.