GeneAnswers (version 2.14.0)

GeneAnswers-class: Class GeneAnswers: contain and describe the relationship between given gene data and specified category

Description

This is a class representation of the relationship between given gene data and specified category.

Creating Objects

Objects can be created using the function geneAnswersBuilder.

Slots

Slot specific to GeneAnswers:

geneInput:

a data frame containing gene Entrez IDs with or without any values. Current version only supports gene Entrez IDs. The values could be foldChange, p value, or other values. These data can be used for concept-gene network. Genes with positive values will be represented as red nodes, while negative value genes are green nodes.

testType:

statistical test method. Current version supports hypergeometric test to test relationship between genes and specified categories.

pvalueT:

the cutoff value of statistical test. Any categories will not be reported if the p value is more than the cutoff.

genesInCategory:

a list containing genes belonging to categories. The names of the list are categories.

geneExprProfile:

a data frame to store gene expression data. If not available, it could be NULL.

annLib:

annotation database used for statistical test.

categoryType:

functional or medical category used for statistical test.

enrichmentInfo:

a data frame containing filtered categories with statistical results by specified pvalueT.

Methods

Class-specific methods:

getGeneInput(GeneAnswers):

Access the geneInput slot of GeneAnswers object.

getTestType(GeneAnswers):

Access the testType slot of GeneAnswers object.

getPValueT(GeneAnswers):

Access the pvaluteT slot of GeneAnswers object.

getGenesInCategory(GeneAnswers):

Access the genesInCategory slot of GeneAnswers object.

getGeneExprProfile(GeneAnswers):

Access the geneExprProfile slot of GeneAnswers object.

getAnnLib(GeneAnswers):

Access the annLib slot of GeneAnswers object.

getCategoryType(GeneAnswers):

Access the categoryType slot of GeneAnswers object.

getEnrichmentInfo(GeneAnswers):

Access the enrichmentInfo slot of GeneAnswers object.

setGeneInput(GeneAnswers, geneInput):

Assign the geneInput slot of GeneAnswers object.

setTestType(GeneAnswers, type=c('hyperG', 'none')):

Assign the testType slot of GeneAnswers object.

setPValueT(GeneAnswers, pvalueT):

Assign the pvaluteT slot of GeneAnswers object.

setGenesInCategory(GeneAnswers, genesInCategory):

Assign the genesInCategory slot of GeneAnswers object.

setGeneExprProfile(GeneAnswers, geneExprProfile):

Assign the geneExprProfile slot of GeneAnswers object.

setAnnLib(GeneAnswers, annLib):

Assign the annLib slot of GeneAnswers object.

setCategoryType(GeneAnswers, type=c('GO', 'GO.BP', 'GO.CC', 'GO.MF', 'DOLITE', 'KEGG', 'REACTOME.PATH', 'CABIO.PATH', 'User defiend')):

Assign the categoryType slot of GeneAnswers object.

setEnrichmentInfo(GeneAnswers, enrichmentInfo):

Assign the enrichmentInfo slot of GeneAnswers object.

summary(GeneAnswers):

Briefly summarize the information of GeneAnswers object and show contents of GeneAnswers object.

show(GeneAnswers):

Briefly show contents of GeneAnswers object.

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('humanExpr')
data('humanGeneInput')
x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneExpressionProfile=humanExpr)
class(x)