EdgeR#
Add to module run order:
#BioModule biolockj.module.rnaseq.EdgeR
Description#
Determine statistically significant differences using edgeR.
Properties#
Properties are the name=value pairs in the configuration file.
EdgeR properties:#
| Property | Description |
|---|---|
| edgeR.designFactors | list A comma-separated list of metadata columns to include as factors in the design forumula used with edgeR. default: null |
| edgeR.designFormula | string The exact string to use as the design the call to model.matrix(). default: null |
| edgeR.scriptPath | file path An R script to use in place of the default script to call edgeR. default: null |
General properties applicable to this module:#
| Property | Description |
|---|---|
| cluster.batchCommand | string Terminal command used to submit jobs on the cluster default: null |
| cluster.jobHeader | string Header written at top of worker scripts default: null |
| cluster.modules | list List of cluster modules to load at start of worker scripts default: null |
| cluster.prologue | string To run at the start of every script after loading cluster modules (if any) default: null |
| cluster.statusCommand | string Terminal command used to check the status of jobs on the cluster default: null |
| docker.saveContainerOnExit | boolean If Y, docker run command will NOT include the --rm flag default: null |
| docker.verifyImage | boolean In check dependencies, run a test to verify the docker image. default: null |
| exe.Rscript | executable Path for the "Rscript" executable; if not supplied, any script that needs the Rscript command will assume it is on the PATH. default: null |
| script.defaultHeader | string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash |
| script.numThreads | integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8 |
| script.numWorkers | integer Set number of samples to process per script (if parallel processing) default: 1 |
| script.permissions | string Used as chmod permission parameter (ex: 774) default: 770 |
| script.timeout | integer Sets # of minutes before worker scripts times out. default: null |
Details#
version: 0.0.0
The two methods of expresison the design are mutually exclusive.
edgeR.designFormula is used as an exact string to pass as the design argument to model.matrix(); example: ~ Location:SoilType. edgeR.designFactors is a list (such as "fist,second") of one or more metadata columns to use in a formula. Using this method, the formula will take the form: ~ first + second
The following two lines are equivilent:edgeR.designFormula = ~ treatment + batchedgeR.designFactors = treatment,batch
Advanced users may want to make more advanced modifications to the call to the edgeR functions. The easiest way to do this is to run the module with the default script, and treat that as a working template (ie, see how input/outputs are passed to/from the R script). Modify the script in that first pipeline, and save the modified script to a stable location. Then run the pipeline with edgeR.scriptPath giving the path to the modified script.
Adds modules#
pre-requisite modules
none found
post-requisite modules
none found
Docker#
If running in docker, this module will run in a docker container from this image:
biolockjdevteam/r_edger:v1.3.19
This can be modified using the following properties:
EdgeR.imageOwner
EdgeR.imageName
EdgeR.imageTag
Citation#
R Core Team (2019). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, Volume 26, Issue 1, 1 January 2010, Pages 139–140, https://doi.org/10.1093/bioinformatics/btp616
Module developed by Ivory, Ke and Rosh
BioLockJ v1.4.2