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RforMassSpectrometry book installation script
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| ## 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]) |
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Hello,
When I run the code above I get the following error message:
When I looked into it and ran pxfiles(px), I get:
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.