quantiles_scores: Returns the quantiles of scores following an GOexpress...

In kevinrue/GOexpress-original: Visualise microarray and RNAseq data using gene ontology annotations

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)

kevinrue/GOexpress-original documentation built on May 20, 2019, 9:07 a.m.