Extract genes from a limma-fit object (resulting from an eBayes call) that
are differentially expressed. Two different methods are used for calling
any_probe - at least one probe for that gene must be differentially
all_probes - every probe for that gene must be differentially
expressed (and must be differentially expressed in the same direction).
This doesn't return information about the direction of change, and only
returns a vector of gene symbols or ids, as extracted from the
dataframe in the limma-fit object
A limma fit object (class: MArrayLM) as returned
by eBayes. If the initial model/analysis contained more than one contrast
the user should select a single contrast prior to passing
The name of the column within
The user selects either
Further arguments that are to be passed through
to limma::decideTests. For example, if you want to set the
A subvector of the inidicated 'gene_column' in fit fit$genes annotation dataframe.
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