genegroups_class {FoldGO} | R Documentation |
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.
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
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
# 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)