RforMassSpectrometry book installation script

R4MS_install.R

## Installation instructions for the R for Mass Spectrometry tutorial
##      https://rformassspectrometry.github.io/book/

## Install packages

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("tidyverse", ask = FALSE)
BiocManager::install("factoextra", ask = FALSE)
BiocManager::install("msdata", ask = FALSE)
BiocManager::install("mzR", ask = FALSE)
BiocManager::install("rhdf5", ask = FALSE)
BiocManager::install("rpx", ask = FALSE)
BiocManager::install("MsCoreUtils", ask = FALSE)
BiocManager::install("QFeatures", ask = FALSE)
BiocManager::install("Spectra", ask = FALSE)
BiocManager::install("ProtGenerics", ask = FALSE)
BiocManager::install("PSMatch", ask = FALSE)
BiocManager::install("pheatmap", ask = FALSE)
BiocManager::install("limma", ask = FALSE)
BiocManager::install("MSnID", ask = FALSE)
BiocManager::install("impute", ask = FALSE)
BiocManager::install("RforMassSpectrometry/SpectraVis", ask = FALSE)


## Download data

library(rpx)
px <- PXDataset("PXD000001") ## answer yes if asked to create a cache directory
fn <- "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
mzf <- pxget(px, fn)
px <- PXDataset("PXD022816")
pxget(px, grep("mzID", pxfiles(px))[1:3])
pxget(px, grep("mzML", pxfiles(px))[1:3])