GeneAnswers-class {GeneAnswers} | R Documentation

## 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.

### 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)

[Package GeneAnswers version 2.22.0 Index]