GeneAnswers-class: Class GeneAnswers: contain and describe the relationship...

In GeneAnswers: Integrated Interpretation of Genes

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.

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

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)

GeneAnswers documentation built on Nov. 8, 2020, 4:53 p.m.