SJAracne.prepare: Prepare Data Files for Running SJARACNe

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Prepare Data Files for Running SJARACNe

Description

SJAracne.prepare prepares data files for running SJAracne. SJARACNe is a scalable software tool for gene network reverse engineering from big data. Detailed description and how to run SJARACNe can be found in its GitHub repository. The usage of SJARACNe may be updated and the bash file generated by this function may not fit the version in use (not suit for SJAracne 0.2.0). Please check https://github.com/jyyulab/SJARACNe/ for details.

Usage

SJAracne.prepare(
  eset,
  use.samples = rownames(Biobase::pData(eset)),
  TF_list = NULL,
  SIG_list = NULL,
  SJAR.main_dir = "",
  SJAR.project_name = "",
  IQR.thre = 0.5,
  IQR.loose_thre = 0.1,
  add_options = "",
  geneSymbol_column = NULL
)

Arguments

eset	an ExpressionSet class object, which contains the expression matrix.
use.samples	a vector of characters, the list of sample used to run SJARACNe.
TF_list	a vector of characters, the TF list.
SIG_list	a vector of characters, the SIG list.
SJAR.main_dir	character, the path to save the results generated by SJARACNe.
SJAR.project_name	character, the project name used to label the output directory.
IQR.thre	numeric, the IQR filter threshold to filter all non-driver genes.
IQR.loose_thre	numeric, the IQR filter threshold to filter for all driver(TF/SIG) genes.
add_options	additional option for running SJARACNe.
geneSymbol_column	character, the column name in fdata(eset) which contains gene symbol. If NULL, will use the main ID in exprs(eset) to fulfill the "geneSymbol" column. Default is NULL.

Examples

## Not run: 
network.par <- list()
network.par$out.dir.DATA <- system.file('demo1','network/DATA/',package = "NetBID2")
NetBID.loadRData(network.par=network.par,step='exp-QC')
db.preload(use_level='gene',use_spe='human',update=FALSE)
use_gene_type <- 'external_gene_name' ## this should user-defined !!!
use_genes <- rownames(Biobase::fData(network.par$net.eset))
use_list  <- get.TF_SIG.list(use_genes,use_gene_type=use_gene_type)
#select sample for analysis
phe <- Biobase::pData(network.par$net.eset)
use.samples <- rownames(phe) ## use all samples, or choose to use some samples
prj.name <- network.par$project.name # can use other names, if need to run different use samples
network.par$out.dir.SJAR <- 'test' ## set the directory
SJAracne.prepare(eset=network.par$net.eset,
                 use.samples=use.samples,
                 TF_list=use_list$tf,
                 SIG_list=use_list$sig,
                 IQR.thre = 0.5,IQR.loose_thre = 0.1,
                 SJAR.project_name=prj.name,
                 SJAR.main_dir=network.par$out.dir.SJAR)

## End(Not run)

jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.