tmodLimmaTopTable: tmod's replacement for the limma topTable function
Description
Produce a data frame for all or for selected coefficients of a linear
fit object, including log fold changes, q-values, confidence intervals and
MSD.Usage
tmodLimmaTopTable(f, genelist = NULL, coef = NULL, adjust.method = "BH",
confint = 0.95)
Arguments
f
result of linear model fit produced by limma functions lmFit and eBayes
genelist
A data frame or a character vector with additional
information on the genes / probes
coef
Which coefficients to extract
adjust.method
Which method of p-value adjustment; see "p.adjust()"
confint
Confidence interval to be calculated
Value
- A data frame with all genes.
Details
Produce a data frame for all or for selected coefficients of a linear
fit object, including log fold changes, q-values, confidence intervals and
MSD. For each coefficient, these four columns will be created in the
output file, with the name consisting of a prefix indicating the type of
the column ("msd.", "logFC", "qval", "ci.L", "ci.R") and the name of the
coefficient.