fitNbinomGLMsForMatrix {DESeq} | R Documentation |
This is a low-level function that is wrapped by nbinomGLMTest
.
fitNbinomGLMsForMatrix(counts, sizeFactors, rawScv, modelFormula, modelFrame, quiet = FALSE, reportLog2 = TRUE, glmControl = list() )
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 |
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
# See the code of fitNbinomGLMs for an example.