foldspectest_class {FoldGO} | R Documentation

## FoldSpecTest S4 class

### Description

FoldSpecTest object calculates test on fold-specificity and stores all resulting data needed for further analysis. It takes object which is instance of subclass of AnnotGroups class (e.g. FuncAnnotGroupsTopGO class) as a minimal set of input parameters. For more details see Constructor section.

### Constructor

`FoldSpecTest(annotgroups, fdrstep1, fdrstep2, padjmethod, fisher_alternative)`, where:

  `annotgroups` - object of FuncAnnotGroups class

  `fdrstep1` - FDR threshold for 1 step of fold-specificty recognition procedure

  `fdrstep2` - FDR threshold for 2 step of fold-specificty recognition procedure

  `padjmethod` - method for multiple testing correction (to see all possible methods print: p.adjust.methods) Benjamini-Hochberg by default

  `fisher_alternative` - indicates the alternative hypothesis and must be one of "two.sided", "greater" or "less". You can specify just the initial letter. Only used in the 2 by 2 case.

### Accessors

In the code examples below `object` is an object of FoldSpecTest class

  `getFStable(object)` - returns dataframe with fold-change-specific terms and related data

  `getNFStable(object)` - returns dataframe with not fold-change-specific terms and related data

  `getResultTable(object)` - returns dataframe with both fold-change-specific and not fold-change-specific terms

  `getWholeIntName(object)` - returns name of largest fold-change interval (DEGs interval)

### Examples

    # FoldSpecTest function requires only object of FuncAnnotGroups class as a
    # minimal set of parameters. In the example up_annotobj is an object of FuncAnnotGroups class
    # compiled from lists of up-regulated genes from rna-seq experiment on auxin treatment
    # of Arabidopsis thaliana roots [FoldGO::up_annotobj].
    FoldSpecTest(up_annotobj)

    # FoldSpecTest function with custom parameters
    fs_up <- FoldSpecTest(up_annotobj, fdrstep1 = 0.2, fdrstep2 = 0.01, padjmethod = "BY")

    # get dataframe with fold-change-specific terms
    getFStable(fs_up)

    # get dataframe with not fold-change-specific terms
    getNFStable(fs_up)

    # get dataframe with both fold-change-specific and not fold-change-specific terms
    getResultTable(fs_up)

    # get name of largest fold-change interval (DEGs interval)
    getWholeIntName(fs_up)

[Package FoldGO version 1.4.0 Index]