summarise.topTable.updown: Summarise a toptable into the up/down regulated genes

In drmjc/microarrays: A collection of microarray and genomic helper code.

Description

Summarise a toptable into the up/down regulated genes

Usage

  summarise.topTable.updown(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))

Arguments

tt	a limma topTable, or list(topTable)
p.thresh	a vector of p value thresholds, set to NULL to ignore
q.thresh	a vector of adj.P.Val thresholds, set to NULL to ignore.
logFC.thresh	a vector of absolute logFC value thresholds

Value

a data.frame of counts of differentially expressed genes

Author(s)

Mark Cowley

See Also

summarise.topTable, summarise.topTable.list

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