fitNbinomGLMs {DESeq} | R Documentation |
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".
fitNbinomGLMs( cds, modelFormula, glmControl=list() )
cds |
a CountDataSet |
modelFormula |
a formula. The left hand side must be 'count' (not 'counts'!), the right
hand side can involve any column of |
glmControl |
list of additional parameters to be passed to |
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.
Simon Anders (sanders@fs.tum.de)
newCountDataSet
,nbinomGLMTest
, nbkd.sf
# see nbinomGLMTest for an example