Calculate percent conversion

Description

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

Usage

calcPercentConversion(fragments, peaks)

Arguments

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.

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.

Author(s)

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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MassArray)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MassArray/calcPercentConversion.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calcPercentConversion
> ### Title: Calculate percent conversion
> ### Aliases: calcPercentConversion
> ### Keywords: attribute arith
> 
> ### ** Examples
> 
> data(MassArray.example.data)
> conversion.data <- calcPercentConversion(MassArray.example.data$fragments.T, MassArray.example.data$samples[[1]]$peaks)
> mean(conversion.data)
[1] 0.005864446
> 
> # NOTE: conversion control data may already be contained within a MassArrayData object; these data can be accessed and visualized by the following (or alternative) commands
> conversion.data <- unlist(lapply(lapply(MassArray.example.data$samples, slot, "quality.conversion"), median, na.rm=TRUE))
> barplot(conversion.data)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>