![](../logo.png)
tmod's replacement for the limma topTable function
tmodLimmaTopTable.Rd
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.
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
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", "SE", "ci.L", "ci.R") and the name of the coefficient.