OK, this works well. However, it would be nice to not write the .mzML
file, but just hold it temporarily in memory for stripping the
appropraite info out. If I try the following in R, trying to coerce
any output to an R object:
test <- shell(paste("msconvert ", "file.RAW"," --filter ", "\"","index
0","\"",sep=""),intern=T)
msconvert runs ok, but I still get file.mzML saved in the appropriate
directory - it is not held in the R object. Any idea on how I might
do this (other than reading the .mzML file into R, stripping out the
timestamp info, then deleting the file = very messy!)
thnaks
Tony
On Jul 13, 2:56 pm, Matt Chambers <[email protected]>
wrote:
> What is the purpose of the msRun startTime attribute? It's an
> xsd:duration type so using it to store a point in time seems odd. But
> the documentation "The time at which the run was started." clearly seems
> to refer to a point in time.
>
> Andrew, a straightforward compromise here is to use msconvert to write
> out just the file header and the first spectrum in mzML. Something like
> 'msconvert data.RAW --filter "index 0"' should do the trick. Then a
> simple grep/regex over the file should get you the startTimeStamp.
>
> Hope this helps,
> -Matt
>
> trl1 wrote:
> > Thanks for the pointer! Unfortunately, I am using xcms (1.21.7 under
> > R 2.11.1/bioconductor 2.6) to read the .mzXML files, which does not
> > currently support reading .mzML files in the release version - I think
> > it is possible with a custom development build (http://
> > metlinwiki.scripps.edu/mediawiki/index.php/EnableMzMLSupport) , but
> > not (easily) under Windows, which is what I will be using.....
>
> > On Jul 12, 7:47 pm, Eric Deutsch <[email protected]> wrote:
>
> >> If you convert the RAW files to the *mzML* format using msconvert, then
> >> the date will be there in the form:
>
> >> <run id="OR20100622_uk_06_1825_1a_34_1"
> >> defaultInstrumentConfigurationRef="IC1"
> >> startTimeStamp="2010-06-23T01:30:33Z"
> >> defaultSourceFileRef="RAW1">
>
> >> Eric
>
>
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/spctools-discuss?hl=en.
