quantiles_scores {GOexpress} | R Documentation

## Returns the quantiles of scores following an GOexpress analysis.

### Description

Returns a set of quantiles in indicating the scores reached by given proportions of the GO terms.

This function can also be used on the output of `subset_scores()` function as it returns a value formatted identically to the output of the `GO_analyse()` function.

### Usage

    quantiles_scores(result, probs=c(0.9, 0.95, 0.99, 0.999, 0.9999),
        quartiles=FALSE)

### Arguments

`result` | The output of `GO_analyse()` or a subset of it obtained from `subset_scores()`.
`probs` | Numeric vector of probabilities with values in [0,1]. (Values up to 2e-14 outside that range are accepted and moved to the nearby endpoint.) See `quantile`
`quartiles` | A numeric vector of the percentiles for which the scores are desired.

### Value

A named vector of percentiles and corresponding scores.

### Author(s)

Kevin Rue-Albrecht

### See Also

Method `quantile`.

### Examples

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

    # filter for Biological Processes associated with 5+ genes and <=0.05 P-value
    filtered_results <- subset_scores(
        result=AlvMac_results.pVal, total_count=5, p.val=0.05,
        namespace="BP")

    # Quantiles of scores
    quantiles_scores(result=filtered_results)

[Package GOexpress version 1.28.0 Index]