foldspectest_class: FoldSpecTest S4 class

In DanWiebe/FoldGO: Package for Fold-specific GO Terms Recognition

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)

DanWiebe/FoldGO documentation built on May 1, 2020, 11:02 p.m.