uvSignif {mdgsa} | R Documentation

## 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.

### Details

Works as `goLeaves` but without removing redundant terms.

### Value

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

### Author(s)

David Montaner dmontaner@cipf.es

### 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)

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

    ## End(Not run)

[Package mdgsa version 1.12.1 Index]