topRomer: Top Gene Set Testing Results from Romer
In hdeberg/limma: Linear Models for Microarray Data

Description Usage Arguments Details Value Author(s) See Also Examples

Extract a matrix of the top gene set testing results from the romer output.

1	topRomer(x,n=10,alternative="up")

`x`	matrix which is the output from romer.
`n`	number of top gene set testing results to be extracted.
`alternative`	character which can be one of the three possible alternative p values: "up", "down" or "mixed".

This function takes the results from romer and returns a number of top gene set testing results that are sorted by the p values.

matrix, which is sorted by the "up", "down" or "mixed" p values, with the rows corresponding to estimated p-values for the top number of gene sets and the columns corresponding to the number of genes for each gene set and the alternative hypotheses mixed, up, down.

Gordon Smyth and Yifang Hu

romer

There is a topic page on 10.GeneSetTests.