BgetDifferentiallyExpressedGenes: Find Differentially Expressed Genes

In bozdaglab/miRDriver: miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer

Description

This function finds the differentially expressed genes based off of the peak wise files generated in the getRegionWiseGistic function and RNASeq count data. This function uses parallel computation by setting the argument value of *ncore*; the default is *ncore = 2*. The argument *RNAcount* needs to be set to the file path for the RNASeq count data. The argument *mirdirectory* needs to be the same as in all previous functions, the argument *DEgene* can be set as "Up","Down" or "All" for getting up regulated, down regulated or both up and down genes from the GISTIC regions; the default is *DEgene = "All"*.

Arguments

ncore	An integer value that represents the number of cores that the user wants to use (default = 2)
RNACount	a R dataframe of RNA seq count
mirdirectory	a character string for the file path of the directory one wants the results in
DEgene	a character string for specifying up regulated, down regulated or both type of genes by setting "Up","Down" or "All", respectively (default = "All")

Value

Returns nothing

Author(s)

Banabithi Bose

Examples

load(system.file("data", "miRDriverData.RData", package = "miRDriver"))

getDifferentiallyExpressedGenes(ncore = 1, RNACount = Dummy_RnaSeq_Count_Data,
                                mirdirectory = tempdir(), DEgene = "All")

bozdaglab/miRDriver documentation built on Feb. 1, 2022, 1:11 p.m.