MassArray (version 1.24.0)

calcPercentConversion: Calculate percent conversion

Description

Function to calculate percent methylation (wrapper for calcMeth() function) for each identified conversion control

Usage

calcPercentConversion(fragments, peaks)

Arguments

fragments

List of MassArrayFragment objects

peaks

List of MassArrayPeak objects comprising spectral data to be used for conversion control calculations

Value

• 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.

Details

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.

See Also

See Also calcMeth, convControl

Examples

data(MassArray.example.data)
conversion.data <- calcPercentConversion(MassArray.example.data$fragments.T, MassArray.example.data$samples[[1]]$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)