topTableAll: Create a topTable for all coefficients in a limma fit object
In january3/myfuncs: loads a few functions I often need

Create a topTable for all coefficients in a limma fit object

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topTableAll(fit, contrasts = NULL, genelist = NULL, idcoll = NULL,
  sign.fc.col = FALSE, sig.threshold = 1e-05, msd = FALSE,
  ci = FALSE, rawp = FALSE)

For every contrast in fit, the log fold change and q-value (p-value corrected for multiple testing) are calculated with the limma function topTable. These columns are joined to common fields (such as probe ID and gene meta data). topTableAll does not sort the data from the fit object.

A data frame with gene meta data and gene fold changes / q-values. For each contrast "N", columns "logFC.N" and "qval.N" are created (and, optionally, columns "logFC.s.N" and "msd.N").

january3/myfuncs documentation built on April 1, 2020, 4:42 a.m.