uvSignif: Filter significant terms in the univariate gene set analysis.
In mdgsa: Multi Dimensional Gene Set Analysis.

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

Filters the rows in the data.frame returned by uvGsa so that only the enriched blocks are kept.

1 2	uvSignif(gsaout, cutoff = 0.05, pvalue = "padj", statistic = "lor", verbose = TRUE, sort = TRUE)

`gsaout`	data.frame; output from uvGsa.
`cutoff`	p-value cutoff for considering significant a Gene Set.
`pvalue`	p-value column to be used. Default is named "padj" as in uvGsa output.
`statistic`	name of the column containing the log odds ratio from the uvGsa analysis.
`verbose`	verbose
`sort`	if TRUE the output data.frame is ordered according to significance.

Works as goLeaves but without removing redundant terms.

The input data.frame but keeping just the 'significant' functional blocks.

David Montaner dmontaner@cipf.es

uvGsa, uvPat, propagateGO, pval2index, goLeaves

uvGsa.res <- as.data.frame (list (N    = c (10, 20, 30, 40),
                                  lor  = c (1.45, -0.32, 1.89, -1.66),
                                  pval = c (0.001, 0.002, 0.05, 0.06)))
uvGsa.res[,"padj"] <- p.adjust (uvGsa.res$pval, "BY")
uvGsa.res
uvSignif (uvGsa.res)

## Not run: 
res <- uvGsa (rindex, annotList)
uvSignif (res)

## End(Not run)