This vignette serves as a guide for R users to use a custom CV before creating an mzQC document.
Warning: you should settle on a CV before instantiating any mzQC objects, since this ensures that all CV terms are consistent (and checked for existance) and that the CV meta information within the mzQC document is accurate.
Target Audience: R users
Let's first consider what happens by default:
library(rmzqc) print(getCVInfo()) ## test if the default CV is usable toQCMetric(id = "MS:4000059", value = 13405) ## number of MS1 scans
However, if you happen to run this code without an internet connection, it will fall back to the PSI-MS CV which is shipped with the rmzqc package (which may not contain the latest CV terms)
## With internet: myCV = getCVSingleton() myCV$setData(getCVDictionary("latest")) ## this is done internally by default when you load the package cat("Number of entries in latest CV: ", nrow(getCVSingleton()$getCV()), "\n") print(getCVInfo()) ## simulate missing internet connection by invoking the function manually myCV$setData(getCVDictionary("local")) cat("Number of entries in local CV: ", nrow(getCVSingleton()$getCV()), "\n") print(getCVInfo())
Now, the package's PSI-MS CV might still not suit you, and you want to use the latest unpublished CV, which you downloaded somewhere, or which you handcrafted for testing. Then simply use a custom .obo file:
myOBO = system.file("./cv/psi-ms.obo", package="rmzqc") ## we will use a local file, but you can point to anything you have (even URI's) myCV$setData(getCVDictionary("custom", myOBO)) cat("Number of entries in custom CV: ", nrow(getCVSingleton()$getCV()), "\n") print(getCVInfo()) ## you may want to change the CV-entries, or URI or version manually, before creating an mzQC file: newCV = list(CV = myCV$getData()$CV, URI = "https://myURI.com", version = "9.9.2") myCV$setData(newCV) print(getCVInfo())
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