findGO: Find top Gene Ontology terms for given genes.

In lidiaad/GOpro: Find the most characteristic gene ontology terms for groups of human 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)

lidiaad/GOpro documentation built on May 21, 2019, 6:13 a.m.