The usage is explained in ./R/main.R
. The main step is to create a JSON file as described below, and edit the parameters at the top of the R script.
Parameters to edit:
# json filename
inputFile <- "sample.json"
# output filename for RData
outputFile <- "sampletable.RData"
# log file
logFile <- "sample.log"
Each experiment (comparison) is considered to be a JSON object, with the parameters "geoSeries", "description", "controlSamples", and "experimentalSamples". The values for each parameter should be a string. "geoSeries" describes the GEO Series identifier. "description" should be a unique description or descriptor for the experiment. "controlSamples" defines the normal sample(s), and "experimentalSamples" defines the experimental sample(s).
The JSON file is an array of experiments.
Sample JSON input:
[{
"geoSeries": "GSE35330",
"description": "Experiment 1",
"controlSamples": ["GSM866121", "GSM866122", "GSM866124", "GSM866126"],
"experimentalSamples": ["GSM866111", "GSM866116", "GSM866118", "GSM866119"]
}
]
Utilized Boris Steipe's GEO expression analysis code: https://github.com/hyginn/zu
https://github.com/hyginn/zu/blob/master/inst/scripts/expressionAnalysisSampleCode.R