This is a internal function. Used by the package to take a formatted dataframe and analyzes it based on the user inputted values.
analyze(analyzeData, multiProbes, windowSize, stepSize, windowStyle, filterData, normalizeData, controlColumn)
| analyzeData | dataframe to be analyzed |
|---|---|
| multiProbes | Option to select what to do with multiple probes to a single gene, default=mean |
| windowSize | Option to alter the size of the windows to be created from the dataframe, default=200 |
| stepSize | Option to alter the size of the steps used to create the windows, default=40 |
| windowStyle | Option to alter the method used to create windows, default=mean |
| filterData | Option to filter data using edgeR::cpm, default=TRUE |
| normalizeData | Option to normalize data using preprocessCore::normalize.quantiles, default=TRUE |
| controlColumn | column of the data used as a control for the statistical analyses |
returns the simplified data