Build an object of a GeneAnswers class

Description

A function to build an object of a GeneAnswers class based on given information.

Usage

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geneAnswersBuilder(geneInput, annotationLib, categoryType = NULL, testType = c("hyperG", "none"), known=TRUE, totalGeneNumber=NULL, geneExpressionProfile = NULL, categorySubsetIDs = NULL, pvalueT = 0.01, FDR.correction = FALSE, verbose=TRUE, sortBy=c('pvalue', 'geneNum', 'foldChange', 'oddsRatio', 'correctedPvalue', 'none'), ...)

Arguments

geneInput

a dataframe containing gene IDs and possible values associated with given gene IDs.

annotationLib

name of given annotation library file or user provided annotation list.

categoryType

name of given annotation category or NULL for user provided annotation list.

testType

name of enrichment test.

known

logic, specify only known annotation gene enrichment test.

totalGeneNumber

number of total genes to perform hypergeometric test.

geneExpressionProfile

data frame containing gene expression file or NULL.

categorySubsetIDs

a character vector of user-specified subset of categories to be tested.

pvalueT

p-value threshold of the enrichment test.

FDR.correction

logic, indicating if FDR correction of the enrichment test p-value is performed or not.

verbose

logic, display current building stage.

sortBy

sorted type

...

additional arguments passed to getGOList.

Details

As the input of geneAnswersBuilder, geneInput could be a character vector (Gene Entrez ID vector), a matrix or a dataframe. For the matrix and dataframe, the first column is for Gene Entrez IDs, while other columns could be any interested values that could be used to represent gene expression direction for generating concepts-genes network. Rownames are not necessary.

annotationLib could be Disease Ontology library, Entrez annotation libraries for a specie, such as 'org.Hs.eg.db'. Current version supports "org.Ag.eg.db", "org.Bt.eg.db", "org.Ce.eg.db", "org.Cf.eg.db", "org.Dm.eg.db", "org.Dr.eg.db", "org.EcK12.eg.db", "org.EcSakai.eg.db", "org.Gg.eg.db", "org.Hs.eg.db", "org.Mm.eg.db", "org.Mmu.eg.db", "org.Pt.eg.db", "org.Rn.eg.db", "org.Ss.eg.db", "org.Xl.eg.db", "org.At.tair.db", "org.Pf.plasmo.db" and "org.Sc.sgd.db". User can also use own annotation library. User's annotation library should be a list. Each element in this list is a vector of genes for a user-specified category. Names of this annotation list are categories' names.

categoryType could be "GO", "GO.BP", "GO.CC", "GO.MF", "DOLITE", "KEGG", "REACTOME.PATH" and "CABIO.PATH". "GO.BP" only test biological process Gene Ontology terms, "GO.CC" for cellular components, "GO.MF" for molecular functions, "GO" for all of these three categories, "KEGG" for all KEGG pathways, and "REACTOME.PATH" for all REACTOME pathways. For user provided annotation library, it should be NULL in most cases.

"caBIO.PATH", which was for NCI-Nature curated, Biocarta and REACTOME, is not supported starting this version because of the termination of caBig project.

If known is set to TRUE, the enrichment test only considers the genes with annotation. If FALSE, the total number of genes in that species will be returned. If user has own annotationLib, totalGeneNumber should be an integer, or one of "anopheles", "arabidopsis", "bovine", "worm", "canine", "fly", "zebrafish", "ecolistraink12", "ecolistrainsakai", "chicken", "human", "mouse", "rhesus", "malaria", "chimp", "rat", "yeast", "pig" and "xenopus". NULL only works when "known" is set TRUE. geneAnswersBuilder will automatically assign the corresponding value to totalGeneNumber. User can get total gene numbers by getTotalGeneNumber, too.

sortBy could be one of "geneNum", "pvalue", "foldChange", "oddsRatio", "correctedPvalue" and "none". Default value is 'pvalue'.

Value

A GeneAnswers class containing geneInput, entrichmentInfo, etc.

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

getTotalGeneNumber

Examples

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data('humanExpr')
data('humanGeneInput') 
x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='h', pvalueT=0.1, FDR.correct=TRUE, geneExpressionProfile=humanExpr)
class(x)

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