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])

Hello,
When I run the code above I get the following error message:

library(rpx)
px <- PXDataset("PXD000001") ## answer yes if asked to create a cache directory
Loading PXD000001 from cache.
fn <- "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
mzf <- pxget(px, fn)
Error in .local(object, ...) : No files to download.

When I looked into it and ran pxfiles(px), I get:

pxfiles(px)
Project PXD000001 files (2):
[remote] PRIDE_Exp_Complete_Ac_22134.pride.mgf.gz
[remote] PRIDE_Exp_Complete_Ac_22134.pride.mztab.gz

It states that there are only 2 files in PXD000001 instead of the 11 files stated In the R for Mass Spectrometry course. Unfortunately, the file(s) that are used in the course are not in PXD000001.