calcPercentConversion: Calculate percent conversion
In MassArray: Analytical Tools for MassArray Data

Description Usage Arguments Details Value Author(s) See Also Examples

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

1	calcPercentConversion(fragments, peaks)

`fragments`	List of MassArrayFragment objects
`peaks`	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.

Reid F. Thompson (rthompso@aecom.yu.edu), John M. Greally (jgreally@aecom.yu.edu)

See Also calcMeth, convControl

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)