foldspectest_class {FoldGO} | R Documentation |
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.
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.
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)
# 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)