uvPat {mdgsa} | R Documentation

## Uni-Variate Gene Set Analysis Pattern Classification.

### Description

Classifies significant patterns form a Uni-Variate Gene Set Analysis.

### Usage

    uvPat(gsaout, cutoff = 0.05, pvalue = "padj", statistic = "lor")

### 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.

### Details

Sign of the 'lor' and p-value are used to define functional blocks as up-regulated, down-regulated or not enriched.

### Value

A numeric vector (values: -1, 0, 1) indicating relationship between the Gene Set and the ranking variable:

1:

  indicates that the gene set is significantly associated to high values of the ranking statistic.

-1:

  indicates that the gene set is significantly associated to low values of the ranking statistic.

0:

  indicates that the gene set not related to the ranking statistic (no enrichment).

### Author(s)

David Montaner dmontaner@cipf.es

### See Also

`uvGsa`, `mdPat`

### 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

    uvGsa.res[,"pat"] <- uvPat (uvGsa.res)
    uvGsa.res

[Package mdgsa version 1.19.0 Index]