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

Description Usage Arguments Author(s) See Also

Export the DE genes from a topTable. Get the DE genes passing various P or Q value threhsolds, and export them to a xls file.

  export.DEgenes.topTable(tt, file = NULL,
    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)

`tt`	a top.table, or a list of top tables
`file`	the path to the output tsv file
`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?