gx.ebarraysWorkflow: Runs the workflow _Compute differentially expressed genes...

In genexplain/geneXplainR: An R interface for the geneXplain platform

Runs the workflow Compute differentially expressed genes using EBarrays

Description

This function computes differentially expressed genes using EBarrays.

Usage

gx.ebarraysWorkflow(inputTable, probeType = "Probes: Affymetrix",
  species = "Human (Homo sapiens)", controlName = "Control",
  controlColumns = c(), conditions = list(), resultFolder,
  skipCompleted = T, wait = T, verbose = F)

Arguments

inputTable	input table with expression data
probeType	type of probes
species	species of the input track genome
controlName	name for the control column group
controlColumns	list of control column names
conditions	a list with condition names and columns
resultFolder	path of result folder
skipCompleted	skip already completed steps
wait	set true to wait for the analysis to complete
verbose	set true for more progress info

Details

A list of column names that make up the control condition is necessary. Furthermore, there must be at least one more condition in conditions list parameter. At most four conditions (besides the control) can be considered. Their names are specified within the list like group_2="name of second group", ..., group_5=.... Note that there is no group_1. Furthermore, one needs to assign columns of the input table to conditions (groups). This information is provided within the same parameter list like Columns_group_2=c("first column name for group_2",...), Columns_group_3=c(...).

Value

the job id of the submitted task. The job id can be used to retrieve information about the status of the analysis.

genexplain/geneXplainR documentation built on Oct. 24, 2023, 8:56 a.m.