October 2019
Intermediate to advanced
316 pages
9h 45m
English
Content preview from R Bioinformatics Cookbook
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How to do it...
Proteomics data can be viewed in a genome browser using the following steps:
- Load the libraries:
library(MSnID)library(EnsDb.Hsapiens.v86)library(rtracklayer)
- Create and populate the search file object:
msnid <- MSnID() msnid <- read_mzIDs(msnid, file.path(getwd(), "datasets", "ch6", "HeLa_180123_m43_r2_CAM.mzid.gz"))
- Extract rows containing useful hits and columns containing useful information:
real_hits <- msnid@psms[! msnid@psms$isDecoy, ]
required_info <- real_hits[, c("spectrumID", "pepSeq", "accession", "start", "end")]
- Extract the Uniprot IDs from the accession column:
uniprot_ids <- unlist(lapply(strsplit(required_info$accession, "\\|"), function(x){x[2]}) ) uniprot_ids <- uniprot_ids[!is.na(uniprot_ids)] ...Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.