quantiles_scores


    The output of <code>GO_analyse()</code> or a subset of it obtained from
    <code>subset_scores()</code>.
    

result


    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 <code>quantile</code>
    

probs


    A numeric vector of the percentiles for which the scores are desired. 
    

quartiles


Returns a set of quantiles in indicating the scores reached by given
proportions of the GO terms.<p></p><p>This function can also be used on the output of <code>subset_scores()</code>
function as it returns a value formatted identically to the output of the
<code>GO_analyse()</code> function.
</p>

 GOexpress 

The package contains methods to visualise the expression profile
of genes from a microarray or RNA-seq experiment, and offers a
supervised clustering approach to identify GO terms containing genes
with expression levels that best classify two or more predefined groups of
samples. Annotations for the genes present in the expression dataset may
be obtained from Ensembl through the biomaRt package, if not provided by
the user. The default random forest framework is used to evaluate the
capacity of each gene to cluster samples according to the
factor of interest. Finally, GO terms are scored by averaging the
rank (alternatively, score) of their respective gene sets to cluster
the samples. P-values may be computed to assess the significance of GO
term ranking. Visualisation function include gene expression profile,
gene ontology-based heatmaps, and hierarchical clustering of
experimental samples using gene expression data.

Kevin Rue-Albrecht

GOexpress

Visualise microarray and RNAseq data using gene ontology annotations

quantiles_scores function


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 <code>subset_scores()</code>
function as it returns a value formatted identically to the output of the
<code>GO_analyse()</code> function.


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

Description

Usage

Arguments

Value

See Also

Examples