- Add related unit tests and documentation.
jotsetung authored on 03/08/2017 04:29:28
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+test_runStartTimeStamp_pwiz <- function() {
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+ ## Works on (some) mzML, what with mzXML? |
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+ library(msdata) |
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+ library(mzR) |
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+ f <- system.file("lockmass/LockMass_test.mzXML", package = "msdata")
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+ fh <- mzR::openMSfile(f) |
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+ run_info <- runInfo(fh) |
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+ checkTrue(any(names(run_info) == "startTimeStamp")) |
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+ checkTrue(is.na(run_info$startTimeStamp)) |
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+ mzR::close(fh) |
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+ |
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+ f <- system.file("microtofq/MM14.mzML", package = "msdata")
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+ fh <- mzR::openMSfile(f) |
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+ run_info <- runInfo(fh) |
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+ checkTrue(any(names(run_info) == "startTimeStamp")) |
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+ checkTrue(is.na(run_info$startTimeStamp)) |
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+ mzR::close(fh) |
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+ |
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+ f <- system.file("microtofq/MM8.mzML", package = "msdata")
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+ fh <- mzR::openMSfile(f) |
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+ run_info <- runInfo(fh) |
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+ checkTrue(any(names(run_info) == "startTimeStamp")) |
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+ checkTrue(!is.na(run_info$startTimeStamp)) |
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+ checkTrue(is.character(run_info$startTimeStamp)) |
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+ mzR::close(fh) |
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+ |
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+ f <- system.file("proteomics/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz", package = "msdata")
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+ fh <- mzR::openMSfile(f) |
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+ run_info <- runInfo(fh) |
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+ checkTrue(any(names(run_info) == "startTimeStamp")) |
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+ checkTrue(!is.na(run_info$startTimeStamp)) |
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+ checkTrue(is.character(run_info$startTimeStamp)) |
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+ mzR::close(fh) |
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+} |
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+ |
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+test_runStartTimeStamp_cdf <- function() {
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+ ## Can not extract from CDF |
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+ f <- system.file("cdf/ko15.CDF", package = "msdata")
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+ fh <- mzR::openMSfile(f, backend = "netCDF") |
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+ run_info <- runInfo(fh) |
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+ checkTrue(any(names(run_info) == "startTimeStamp")) |
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+ checkTrue(is.na(run_info$startTimeStamp)) |
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+ mzR::close(fh) |
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+} |
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+ |
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+test_runStartTimeStamp_ramp <- function() {
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+ ## Can not extract from ramp |
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+ f <- system.file("iontrap/extracted.mzData", package = "msdata")
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+ fh <- mzR::openMSfile(f, backend = "Ramp") |
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+ run_info <- runInfo(fh) |
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+ checkTrue(any(names(run_info) == "startTimeStamp")) |
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+ checkTrue(is.na(run_info$startTimeStamp)) |
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+ mzR::close(fh) |
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+} |
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+ |
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+ |
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@@ -55,7 +55,10 @@ para(object) |
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Accessors to the analytical setup metadata of a run. |
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\code{runInfo} will show a summary of the experiment as a named list,
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including \code{scanCount}, \code{lowMZ}, \code{highMZ},
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- \code{dStartTime} and \code{dEndTime}.
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+ \code{dStartTime}, \code{dEndTime} and \code{startTimeStamp}. Note
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+ that \code{startTimeStamp} can only be extracted from \emph{mzML}
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+ files using the \emph{pwiz} backend. A \code{NA} is reported if its
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+ value is not available. |
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The \code{instrumentInfo} method returns a named \code{list} including
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instrument manufacturer, model, ionisation technique, analyzer and |
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detector. \code{mzRpwiz} will give more additional information including
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