fitNbinomGLMsForMatrix: Fit negative binomial GLMs to a count matrix.

In DESeq: Differential gene expression analysis based on the negative binomial distribution

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.

Author(s)

Simon Anders, [e-mail]

Examples

# See the code of fitNbinomGLMs for an example.

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.

DESeq documentation built on April 28, 2020, 6:37 p.m.