summarise.topTable: Summarise a topTable object
In drmjc/microarrays: A collection of microarray and genomic helper code.

Description Usage Arguments Value Author(s)

Get the DE genes from a topTable or topTableQ object, looking in the “P.Value”, and “q” or “logFC” column, returning a data.frame with 1 row, with numbers of DE genes in each column.

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  summarise.topTable(tt, p.thresh = c(0.05, 0.001, 1e-04),
    q.thresh = c(0.25, 0.1, 0.05),
    logFC.thresh = c(0.585, 1, 2))

`tt`	a `topTable` or `topTableQ` object
`p.thresh`	a numberic vector of p-value threhshlds to use. set to NULL if not required.
`q.thresh`	a numeric vector of q-value threhsolds to use. set to NULL if not required
`logFC.thresh`	a numeric vector of absolute logFC threhsolds to use. set to NULL if not required

a 1 x n data.frame, where n = np + nq where np is the number of p-value threhsolds, and nq is the number of q-value thresholds. See also: export.DEgenes.topTable

Mark Cowley, 25/2/2008

drmjc/microarrays documentation built on May 15, 2019, 2:26 p.m.