DEgenes.topTable: Get the DE genes from a topTable. Get the lists of DE genes...
In drmjc/microarrays: A collection of microarray and genomic helper code.

Description Usage Arguments Value Author(s) See Also

Get the DE genes from a topTable. Get the lists of DE genes that pass various P or Q thresholds, see also summarise.topTable

  DEgenes.topTable(tt, p.thresh = c(0.05, 0.001, 1e-04),
    q.thresh = c(0.25, 0.1, 0.05),
    lfc.thresh = c(0.585, 1, 2), values = FALSE,
    as.df = FALSE, direction = c("either", "up", "down"))

`tt`	a top.table, or a list of top tables
`p.thresh`	vectors of thresholds for p.values
`q.thresh`	vectors of thresholds for FDRs
`lfc.thresh`	vector of POSITIVE log base 2 FC thresholds. Note that absolute logFC's are used
`values`	also return the ‘p’/‘q’/‘logFC’ value?
`as.df`	logical if `FALSE` the result will be a list, otherwise will be a `data.frame`
`direction`	Which direction can the gene change be? one of “either”, “up” or “down”