geneOntology: List of informations on Gene Ontology of selected genes

In spell098/rnaseq_app:

Description

List of informations on Gene Ontology of selected genes

Usage

geneOntology(results, go, typeID = "ensembl_gene_id", ngenes)

Arguments

results	A topTable with only the genes considered significant (according to the p-value and logFC limits provided in the function results_topTable)
go	An object that contain all gene ontology informations for every gene
typeID	Type of IDs used as rows in the expression matrix.Default="ensembl_gene_id"
ngenes	A list of WGCNA results

Value

A list of gene ontology informations for all comparisons determinated my the experimental design. For example, if there are 3 groups (a,b,c), 3 comparisons are possible (a-b,a-c,b-c). The object return is a list containing 3 lists named "a-b", etc. Each of these lists contain the following objects:

geneGO.selected

For every gene ontology that imply at least 1 significant gene,

GOarray.percent

GOarray

GOarray_CellComponent

GOarray_MolecularFunction

GOarray_BiologicalProcess

Author(s)

Simon J Pelletier

See Also

annotate_ensembl annotate_geo results_topTable topTable

Examples

results <- readRDS("data/results_LGVD.rds")
go <- read.csv("annotations/go.csv",header=FALSE)
typeID <- "ensembl_gene_id"
colnames(go) = c(typeID,"go_term_name","go_domain")
ngenes <- 26689
ontologyInfos <- geneOntology(results,go,typeID,ngenes)

spell098/rnaseq_app documentation built on May 30, 2019, 7:57 a.m.