getConceptTable: Generate top concepts-genes table
In GeneAnswers: Integrated Interpretation of Genes

Description Usage Arguments Details Value Author(s) References See Also Examples

Function to generate a top concepts-genes table based on a given GeneAnswers instance list.

1	getConceptTable(gAList, topCat=10, items=c('both', 'geneNum', 'pvalue'), sortBy = c('pvalue', 'geneNum', 'foldChange', 'oddsRatio', 'correctedPvalue'), catTerm=TRUE, strict=FALSE)

`gAList`	a GeneAnswers instance list
`topCat`	a numeric or string vector specified categories
`items`	specify the contents in cells, see details
`sortBy`	sorted type
`catTerm`	a logic value to specify whether mapping category IDs to category names
`strict`	logic value to stop conversion if NA is introduced.

A list containing two top concepts-genes tables is generated. The first table consists of gene amounts and enrichment test p values if 'items' is set to 'both'. Only gene amounts are kept if items is set to 'geneNum' or enrichment test p values if it is set to 'p values', while the second table contains enrichment test p values

return a concepts-genes matrix list.

Gang Feng, Pan Du and Simon Lin

Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10

geneAnswersBuilder

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data(sampleGroupsData)
gAKEGGL <- lapply(sampleGroupsData, geneAnswersBuilder, 'org.Hs.eg.db', categoryType='KEGG', pvalueT=0.1, verbose=FALSE)
output<- getConceptTable(gAKEGGL)