genegroups_class: S4 class for Gene Groups

In FoldGO: Package for Fold-specific GO Terms Recognition

Description

This function splits gene list into quantiles and generates all unions of neighbouring quantiles. It takes dataframe with genes ID's and fold values, number of quantiles and logical variable which must set to TRUE if fold values are presented in logarithmic scale, otherwise it must be set to FALSE value (TRUE by default) as parameters.

Constructor

GeneGroups(inputtable, quannumber, logfold), where:

inputtable - dataframe contains initial set of genes gene ID's in the first row and corresponding fold change values in the second row

quannumber - number of quantiles (e.g. 2,3,4...)

logfold - TRUE if fold values are presented in log scale, otherwise is FALSE

Accessors

In the code examples below object is an object of GeneGroups class

getGroups(object) - returns list of gene sets for each quatile and all combinations

getWholeIntName(object) - returns name of the interval containing all differentially expressed genes

getQuanNumber(object) - returns number of quantiles

getIntNames(object) - returns vector of intervals names

getRegType(object) - returns regulation type

Examples

# split initial gene set into quantiles
gene_groups <- GeneGroups(degenes, 6)
# get list of gene sets for each quatile and all combinations
getGroups(gene_groups)
# get name of the interval containing all differentially expressed genes
getWholeIntName(gene_groups)
# get number of quantiles
getQuanNumber(gene_groups)
# get vector of intervals names
getIntNames(gene_groups)
# get regulation type
getRegType(gene_groups)

FoldGO documentation built on Nov. 8, 2020, 7:50 p.m.