GOexpress-package: Visualise microarray and RNAseq data with gene ontology...

Description Details Author(s) See Also Examples


Integrates gene expression data with gene ontology annotations to score and visualise genes and gene ontologies best clustering groups of experimental samples. Supports custom annotations, or alternatively provides an interface to the Ensembl annotations using the biomaRt package. The default scoring approach is based on the random forest framework, while a one-way ANOVA is available as an alteranative. GO term are scored and ranked according to the average rank (alternatively, average power) of all associated genes. P-values can be generated to assess the significance of GO term ranking. The ranked list of GO terms is returned, with tools allowing to visualise the statistics on a gene- and ontology-basis.


Package: GOexpress
Type: Package
Version: 1.7.1
Date: 2016-02-06
License: GPL (>= 3)

This package requires only two input variables

  1. An ExpressionSet containing assayData and phenoData. The former should be a gene-by-sample matrix providing gene expression values for each gene in each sample. The latter should be an AnnotatedDataFrame from the Biobase package providing phenotypic information and grouping factors with two or more levels.

  2. The name of the grouping factor to investigate, which must be a valid column name in the phenoData slot of the above ExpressionSet.

Following analysis, visualisation methods include:


Maintainer: Kevin Rue-Albrecht <kevinrue67@gmail.com>

See Also

Main method for an example usage: GO_analyse.

Packages Biobase, randomForest, RColorBrewer, VennDiagram.

Methods biomaRt:getBM, ggplot2:ggplot, gplots:heatmap.2, gplots:bluered, gplots:greenred, grid:grid.newpage, grid:grid.layout, stringr:str_extract.


# Sample input data available with package:

# Sample output data available with package:

# Supported species and microarrays:

Example output

Loading required package: grid
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

GOexpress documentation built on Nov. 8, 2020, 7:45 p.m.