rerank: Reorder the result variable by alternative metrics.

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/post_analysis.R

Description

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

Usage

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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

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# 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")

kevinrue/GOexpress-original documentation built on May 18, 2017, 7:31 p.m.