analyze: LONGO analysis

In BioHPC/LONGO: Long gene expression as a metric for neuronal identity

LONGO analysis

Description

This is a internal function. Used by the package to take a formatted dataframe and analyzes it based on the user inputted values.

Usage

analyze(analyzeData, multiProbes, windowSize, stepSize, windowStyle, filterData,
  normalizeData, controlColumn)

Arguments

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

Value

returns the simplified data

BioHPC/LONGO documentation built on Oct. 31, 2024, 4:43 a.m.