mdgsa (version 1.4.2)

uvSignif: Filter significant terms in the univariate gene set analysis.

Description

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

Usage

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

Arguments

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.

Value

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

Details

Works as goLeaves but without removing redundant terms.

See Also

uvGsa, uvPat, propagateGO, pval2index, goLeaves

Examples

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)

res <- uvGsa (rindex, annotList)
uvSignif (res)