decideTestsDGE {edgeR} | R Documentation |
Classify a series of related differential expression statistics as up, down or not significant. A number of different multiple testing schemes are offered which adjust for multiple testing down the genes as well as across contrasts for each gene.
decideTestsDGE(object, adjust.method="BH", p.value=0.05)
object |
|
adjust.method |
character string specifying p-value adjustment method. Possible values are |
p.value |
numeric value between 0 and 1 giving the desired size of the test |
These functions implement multiple testing procedures for determining whether each log-fold change in a matrix of log-fold changes should be considered significantly different from zero.
An object of class TestResults
(see TestResults
).
This is essentially a numeric matrix with elements -1
, 0
or 1
depending on whether each DE p-value is classified as
significant with negative log-fold change, not significant or
significant with positive log-fold change, respectively.
Davis McCarthy, Gordon Smyth
Adapted from decideTests
in the limma package.