Nothing
## ----eval=TRUE----------------------------------------------------------------
library(rmzqc)
data = readMZQC(system.file("./testdata/test.mzQC", package = "rmzqc", mustWork = TRUE))
cat("This file has ", length(data$runQualities), " runqualities\n")
cat(" - file: ", data$runQualities[[1]]$metadata$inputFiles[[1]]$name, "\n")
cat(" - # of metrics: ", length(data$runQualities[[1]]$qualityMetrics), "\n")
cat(" - metric #1 name: ", data$runQualities[[1]]$qualityMetrics[[1]]$name, "\n")
cat(" - metric #1 value: ", data$runQualities[[1]]$qualityMetrics[[1]]$value, "\n")
## ----eval=TRUE----------------------------------------------------------------
library(rmzqc)
## we need a proper URI (i.e. no backslashes and a scheme, e.g. 'file:')
## otherwise writing will fail
raw_file = localFileToURI("c:\\data\\special.raw", FALSE)
file_format = getCVTemplate(accession = filenameToCV(raw_file))
ptxqc_software = toAnalysisSoftware(id = "MS:1003162", version = "1.0.13") ## you could use 'version = packageVersion("PTXQC")' to automate further
run1_qc = MzQCrunQuality$new(metadata = MzQCmetadata$new(label = raw_file,
inputFiles = list(MzQCinputFile$new(basename(raw_file),
raw_file,
file_format)),
analysisSoftware = list(ptxqc_software)),
qualityMetrics = list(toQCMetric(id = "MS:4000059", value = 13405) ## number of MS1 scans
)
)
mzQC_document = MzQCmzQC$new(version = "1.0.0",
creationDate = MzQCDateTime$new(),
contactName = Sys.info()["user"],
contactAddress = "test@user.info",
description = "A minimal mzQC test document with bogus data",
runQualities = list(run1_qc),
setQualities = list(),
controlledVocabularies = list(getCVInfo()))
## write it out
mzqc_filename = paste0(getwd(), "/test.mzQC")
writeMZQC(mzqc_filename, mzQC_document)
cat(mzqc_filename, "written to disk!\n")
## read it again
mq = readMZQC(mzqc_filename)
## print some basic stats
gettextf("This mzQC was created on %s and has %d quality metric(s) in total.", dQuote(mq$creationDate$datetime), length(mq$runQualities) + length(mq$setQualities))
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.