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 |
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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