GeneAnswers (version 2.14.0)

getConceptTable: Generate top concepts-genes table

Description

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

Usage

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

Arguments

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.

Value

return a concepts-genes matrix list.

Details

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

References

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

See Also

geneAnswersBuilder

Examples

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