calcPercentConversion {MassArray} | R Documentation |
Function to calculate percent methylation (wrapper for calcMeth()
function) for each identified conversion control
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)