findGO {GOpro} | R Documentation

## Find top Gene Ontology terms for given genes.

### Description

Find top Gene Ontology terms for given genes.

### Usage

    findGO(groups, topAOV = 50, sig.levelAOV = 0.05, parallel = FALSE,
      grouped = "tukey", sig.levelGO = 0.05, minGO = 5, maxGO = 500,
      clust.metric = NULL, clust.method = NULL, dist.matrix = NULL,
      topGO = 3, sig.levelTUK = 0.05, onto = c("MF", "BP", "CC"),
      extend = FALSE, over.rep = FALSE)

### Arguments

`groups` | a MultiAssayExperiment object containing an ExperimentList class object representing gene expressions for at least 3 cohorts. Rows must be named with genes' aliases. The order of samples and genes has to be the same for each ExperimentList class object.
`topAOV` | A numeric value, a number of most significantly differentiated genes to be returned.
`sig.levelAOV` | a numeric value, a significance level used in BH correction for multiple testing (`aovTopTest`).
`parallel` | A logical value indicating if a task should be run on more than one core.
`grouped` | A method of grouping genes, one of 'tukey' and 'clustering'.
`sig.levelGO` | A numeric value, a significance level used in BH correction for multiple testing (`findTopGOs`).
`minGO` | A minimum number of functions that a gene needs to represent to be considered as frequent.
`maxGO` | A maximum number of functions that a gene needs to represent to be considered as frequent.
`clust.metric` | The method to calculate a distance measure used in hierarchical clustering, possible names: "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski".
`clust.method` | The agglomeration method used to cluster genes. This should be #'one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).
`dist.matrix` | A matrix with calculated distances to be used as a metric by `hclust` function.
`topGO` | A number of the most characteristic functions of groups of genes to be returned.
`sig.levelTUK` | A numeric value, a significance level used in Tukey's all pairwise comparison (`groupByTukey`).
`onto` | An ontology or ontologies to be searched for significant GO terms, at least one of 'MF' (molecular function), 'BP' (biological process), and 'CC' (cellular component).
`extend` | A logical value indicating if an extended version of the output should be presented.
`over.rep` | A logical value indicating if an over represented GO terms should be presented in the plot.

### Value

A data frame containing the top gene ontology terms for each group of genes and the gene aliases.

### Examples

    findGO(exrtcga, grouped = 'clustering', topGO = 10, onto = 'MF')
    findGO(exrtcga, grouped = 'tukey', topGO = 2, extend = TRUE)

[Package GOpro version 1.13.0 Index]