Function to calculate percent methylation (wrapper for
calcMeth() function) for each identified conversion control
List of MassArrayFragment objects
List of MassArrayPeak objects comprising spectral data to be used for conversion control calculations
This function serves as a wrapper function for
calcMeth(), such that percent methylation is calculated for all conversion controls within the input list of fragments.
Returns a list of numerical values (from 0 to 1) corresponding to percent methylation for each conversion control, with 0 Note that each element within the returned list will represent conversion control(s) for a single sample, while each element may contain multiple values with each value corresponding to data obtained from a single conversion control fragment.
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data(MassArray.example.data) conversion.data <- calcPercentConversion(MassArray.example.data$fragments.T, MassArray.example.data$samples[]$peaks) mean(conversion.data) # NOTE: conversion control data may already be contained within a MassArrayData object; these data can be accessed and visualized by the following (or alternative) commands conversion.data <- unlist(lapply(lapply(MassArray.example.data$samples, slot, "quality.conversion"), median, na.rm=TRUE)) barplot(conversion.data)
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