In eckartbindewald/bfxapps2: R Bioinformatics Applications

library(dplyr)
library(knitr)
knitr::opts_chunk$set(echo = TRUE,message=FALSE, warning=FALSE)
remote_dir="https://raw.githubusercontent.com/PacktPublishing/R-Bioinformatics-Cookbook/master/datasets/ch6"

Install Packages

if (!require(mzR)) {
  BiocManager::install("mzR")
}
if (!require(MSnbase)) {
  BiocManager::install("MSnbase")
}
if (!require(MSnID)) {
  BiocManager::install("MSnID")
}
if (!require(EnsDb.Hsapiens.v86)) {
  BiocManager::install("EnsDb.Hsapiens.v86")
}
if (!require(protViz)) {
  BiocManager::install("protViz")
}
library(mzR)
library(MSnbase)

2. Load the files into objects

mzxml_file <- "threonine_i2_e35_pH_tree.mzXML" 
if (!file.exists(mzxml_file)) {
  download.file(file.path(remote_dir, mzxml_file), mzxml_file)
}
ms1 <- openMSfile(mzxml_file)
mzdata_file <- "HAM004_641fE_14-11-07--Exp1.extracted.mzdata"
if (!file.exists(mzdata_file)) {
  download.file(file.path(remote_dir, mzdata_file), mzdata_file)
}
ms2 <- openMSfile(mzdata_file)
mzml_file <- "MM8.mzML"
if (!file.exists(mzml_file)) {
  download.file(file.path(remote_dir, mzml_file), mzml_file)
}
ms3 <- openMSfile(mzml_file)

3. View the metadata where available

runInfo(ms3)

4. Plot the spectra:

msn_exp <- MSnbase::readMSData(mzxml_file)
MSnbase::plot(msn_exp, full = TRUE)
MSnbase::plot(msn_exp[5], full = TRUE)

eckartbindewald/bfxapps2 documentation built on Feb. 6, 2025, 3:22 a.m.