rerank {GOexpress} | R Documentation

## Reorder the result variable by alternative metrics.

### Description

Reorder the ranked tables of GO terms and genes either by increasing (average) rank or decreasing (average) score.

### Usage

    rerank(result, rank.by = 'rank')

### Arguments

`result` | The output of `GO_analyse()` or a subset of it obtained from `subset_scores()`.
`rank.by` | Either of 'rank', 'score' or 'p.val'; the metric to rank the GO terms and genes. Note that 'pval' is only applicable on the output of the `pValue_GO()` function. See details for breaking ties.

### Details

Taking an example, to rank GO terms by P-value and break ties by average rank, rerank first by 'rank', and then rerank the resulting object by 'p.val'.

### Value

A list formatted identically to the results of the analysis, but ordered by the chosen metric.

### Note

The name reorder() was not used to avoid conflict with package `stats`.

### Author(s)

Kevin Rue-Albrecht

### See Also

Method `GO_analyse`.

### Examples

    # load the sample output data
    data(AlvMac_results)

    # Re-rank the GO terms and genes based on the actual score instead of the rank
    reranked.byScore <- rerank(result=AlvMac_results, rank.by="score")

    # load the sample output data with p.values computed
    data(AlvMac_results.pVal)

    # To rank by P-value, while breaking the ties by ave_rank,
    # rank first by ave_rank
    reranked.byRank <- rerank(result=AlvMac_results.pVal, rank.by="rank")
    # rank the result by P-value
    reranked.pVal_rank <- rerank(result=reranked.byRank, rank.by="p.val")

[Package GOexpress version 1.28.0 Index]