fitNbinomGLMs: Fit a generalized linear model (GLM) for each gene.

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

Description

Use this function to estimate coefficients and calculate deviance from a GLM for each gene. The GLM uses the nbkd.sf family, with the dispersion estimate according to getVarianceFunction(cds). Note that this requires that the variance functions were estimated with method "pooled" or "blind".

Usage

fitNbinomGLMs( cds, modelFormula, glmControl=list() )

Arguments

cds	a CountDataSet
modelFormula	a formula. The left hand side must be 'count' (not 'counts'!), the right hand side can involve any column of pData(cds), i.e., pData(cds) is used as the model frame. If you have passed just a single factor to the 'conditions' argument of newCountDataSet, it can be referred to as 'condition' in the formula. If you have passed a data frame to 'conditions', all columns of this data frame will be available.
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])

See Also

newCountDataSet,nbinomGLMTest, nbkd.sf

Examples

   # see nbinomGLMTest 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.