EgetTransGenePredictorFile: Creation of the trans gene predictor file

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

Description

This function creates a TransGenePredictorFile for each trans gene based on the miRNA and DE cis files from the output of the *gatherCisGenes* function and the user provided dataframes *methylationData*, *RSeqData*, *CNVData*, *TFData*, *mirnaData*. The five dataframes needed for this function are described in the example datasets section. The TransGenePredictorFiles will contain information about the possible predictors for each patient based on the data provided. The TransGenePredictorFiles will be saved in the file path ~/mirdirectory/mirDriverFold/miRDriver_Step4/TransGenePredFile/. As always mirdirectory in the file path represents the mirdirectory chosen for the analysis and should be the same as the mirdirectory used in all previous functions.For *TFData*, the "Confidence" column can work with integers or numeric values and is supposed to filter the interactions based on a minimum threshold that we set as "minConfidence = 5" as default.

Arguments

ncore	An integer value that represents the number of cores that the user wants to use (default = 2)
methylationData	a dataframe for the methylation data
RSeqData	a dataframe for the RNA sequence data
CNVData	a dataframe for the copy number varation data
TFData	a dataframe for the transcription factor data
mirnaData	a dataframe for the mirna data
mirdirectory	a character string for the file path of the directory one wants the results in
minConfidence	an integer or numeric value for the *TFData* for filtering the "Confidence" column which is supposed to filter the interactions based on a minimum threshold that we set as "minConfidence = 5" as default

Value

Returns nothing

Author(s)

Banabithi Bose

Examples

load(system.file("data", "miRDriverData.RData", package = "miRDriver"))
getTransGenePredictorFile(
  ncore = 1,
  methylationData = dummy_methylationData10,
  RSeqData = dummy_RSeqData10_200,
  CNVData = dummy_CNVData10,
  TFData = dummy_TFData,
  mirnaData = dummy_mirnaData10,
  mirdirectory = tempdir()
)

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