View the GOseq pathway analysis after having run Goseq, or search for a term.

Description

Having defined at least one genomic module using runSpinglass or runBioNet, this function allows you to interrogate the enriched terms for a specific module or combination of modules.

Usage

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extractGOseq(pvalue_annotation, which_network = NULL)
searchGOseq(pvalue_annotation, search_string, wholeword = FALSE)

Arguments

pvalue_annotation

An S4 object of class PvalueAnnotation, for which module-finding and GOseq analysis have already been performed

which_network

A numeric vector of a length of at least one, corresponding to a particular functional module specifically for the extract function.

search_string

A character specfying a search string specifically for the search function.

wholeword

A logical (TRUE/FALSE) detemring whether the search string must be matched for whole word specifically for the search function.

Details

Goseq analysis is useful since it allows you to assess term/pathway enrichment in a collection of genes, while adjusting for bias data. Potential bias can be from aspects like gene length or probe density that influence the likelihood of finding a particular gene. For more information please see the goseq reference.

Value

##Extract## A list with eahc element matching the specified module. Has columns identfying the term id, the over represented p-value, underrepresented p-value the total number in the category found in the module, the total number in the category and a more descirptive pathway name.

##Search## A matrix with columns identfying the module name, module position/significance , the specific enriched term, the rank of that term within all enriched terms and the total number of enriched terms.

Author(s)

N. Ari Wijetunga

References

Young MD, Wakefield MJ, Smyth GK and Oshlack A (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology, 11, pp. R14.

See Also

runGOseq runSpinglass runBioNet extractModules plotModule

Examples

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## Commented out below.  See vignette for more details ##

##load sample data with only PvalueObject filled in##
data(test_annotation_score_data)

## show goseq analysis for module 1 ##
extractGOseq(test_annotation, 1)

## show goseq analysis for module 1 and 2 ##
#extractGOseq(test_annotation, 1:2)

## search for term ##

#searchGOseq(test_annotation, "Cell cycle")

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