Generate top concepts-genes table

Share:

Description

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

Usage

1
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.

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

Value

return a concepts-genes matrix list.

Author(s)

Gang Feng, Pan Du and Simon Lin

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

1
2
3
data(sampleGroupsData)
gAKEGGL <- lapply(sampleGroupsData, geneAnswersBuilder, 'org.Hs.eg.db', categoryType='KEGG', pvalueT=0.1, verbose=FALSE)
output<- getConceptTable(gAKEGGL)  

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.