Peaksorter is a R package for sorting LC-MS peak lists to prioritize peaks of interest.
Example uses:
- to reduce datasets for sample classification
- to select peaks for further investigation
- to evaluate different peak sorting methods
- Download and install R version 2.10 or higher. Link
- In R, run the following code to install prerequisites and this package:
# Install prerequisite packages
install.packages(c('ggplot2', 'ROCR'))
# Install PeakSorter from GitHub
library(devtools)
install_github("agentlans/PeakSorter")
Let peak.data.frame be a data frame where:
- each row represents a LC-MS peak
- and columns are Rt, Mz, Intensity, Name
- representing retention time (min.), m/z, intensity, and peak ID, respectively
Then to sort the peaks using the binned method, run the following code:
sorted.list <- bin.prioritize(peak.data.frame)
To view the top 10 peaks, run:
top.peaks(sorted.list, 10)
For more information, please see the package vignettes:
vignette("Idh1", package="PeakSorter")
The GNU General Public License v3.0
Software maintainer: Alan Tseng