gx.limmaWorkflow: 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 Limma

Description

This function computes differentially expressed genes using Limma. Limma output tables (one for each condition pair) are located in the result folder named after the compared conditions.

Usage

gx.limmaWorkflow(inputTable, probeType = "Probes: Affymetrix",
  species = "Human (Homo sapiens)", 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
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

The conditions need to be specified in the corresponding list parameter. There can be up to five different conditions. Their names are specified within the list like Condition_1="name of first condition", ..., Condition_5=.... Furthermore, one needs to assign columns of the input table to conditions. This information is provided within the same parameter list like 1_Columns=c("first column name for condition 1",...), 2_Columns=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.