DgatherCisGenes: Gathering of Cis genes for each trans gene

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

Description

This function collects all the DE cis genes and all miRNAs for each trans gene. This function uses the output from the *makingCisAndTransGene()* function as well as a *mirna_bedfile* and a *gistic_bedfile*. The gistic_bedfile is described in the makingCisAndTransGene function description and can be made using the *getRegionWiseGistic()* function. The *mirna_bedfile* is described in the example datasets section and needs to be provided by the user. The output from this function is in the folders gene_all_DEcis and gene_all_mirna. In these folders there is a folder for each trans gene where all the miRNA's or DE cis genes are listed. As with all the functions the mirdirectory needs to be consistent with the other functions.

Arguments

ncore	An integer value that represents the number of cores that the user wants to use (default = 2)
mirna_bedfile	A dataframe in the format of a bedfile for all of the micro RNA
gistic_bedfile	A dataframe in the format of a bedfile for the gistic results
mirdirectory	a character string for the file path of the directory one wants the results in

Value

Returns nothing

Author(s)

Banabithi Bose

Examples

load(
  file.path(
    tempdir(),
    "mirDriverFold",
    "miRDriver_Step1",
    "GisticResults",
    "gistic_bedfile.rda"
  )
)

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

gatherCisGenes(
  ncore = 1,
  mirna_bedfile = mirna_bedfile,
  gistic_bedfile = region,
  mirdirectory = tempdir()
)

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