GOexpress (version 1.6.1)

rerank: 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.

Value

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

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'.

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")