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writeMgfData doesn't work for MS1 #73

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meowcat opened this issue Dec 17, 2015 · 1 comment
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writeMgfData doesn't work for MS1 #73

meowcat opened this issue Dec 17, 2015 · 1 comment

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@meowcat
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meowcat commented Dec 17, 2015

Hi,

These lines in writeMgfContent make writeMgfData fail on MS1 spectra:

  .cat("\nRTINSECONDS=", rtime(sp), "\nPEPMASS=", precursorMz(sp))

  if (length(precursorCharge(sp)) && !is.na(precursorCharge(sp))) {
    .cat("\nCHARGE=", precursorCharge(sp), "+")
  }
d> writeMgfData(cpds.tot[[1]]@parent)
Error in precursorMz(sp) : No precursor MZ value for MS1 spectra.

Admittedly my Spectrum1 objects are not created by MSnbase directly but by RMassBank, but I think this should still work...
lgatto pushed a commit that referenced this issue Dec 18, 2015
@LaurentGatto
Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by m…
1b8adc1 
…eowcat)
@lgatto
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lgatto commented Dec 18, 2015

@meowcat - thanks for the report. Should be fixed in version 1.19.7 and available via biocLite("MSnbase") within 24 hours or immediately from github with biocLite("lgatto/MSnbase").

@lgatto lgatto closed this as completed Dec 18, 2015
@meowcat meowcat mentioned this issue Dec 18, 2015
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lgatto pushed a commit that referenced this issue May 4, 2016
Merge branch 'master' into devel
58b0aea 
* master:
  Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by meowcat)
  remove spurious call to browser
  note on sort(i) in pSet,[
  fix missing paren
  feature names testing
  new sampleNames<- for pSet/MSnExp objects
  new devel version

From: Laurent <[email protected]>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@111609 bc3139a8-67e5-0310-9ffc-ced21a209358
lgatto pushed a commit that referenced this issue May 4, 2016
Merge branch 'master' into devel
2d21cf4 
* master: (860 commits)
  selective ggplot2 import
  typos and spaces
  fixed typos in Rd files
  readMSnSet2 now also accepts a data.frame as input
  no empty new line
  new devel version
  Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by meowcat)
  remove spurious call to browser
  note on sort(i) in pSet,[
  fix missing paren
  feature names testing
  new sampleNames<- for pSet/MSnExp objects
  new devel version
  bump version and update NEWS to document latest PRs
  change spectrum order to natural sorting (add missing MS2 level); #69
  change spectrum order to natural sorting
  upate style
  update news
  rewrite featureCV
  add colSd to calculate sd column-wise
  ...

From: Laurent <[email protected]>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@113063 bc3139a8-67e5-0310-9ffc-ced21a209358
lgatto pushed a commit that referenced this issue Oct 27, 2016
Merge branch 'master' into devel
b3feb08 
* master: (860 commits)
  selective ggplot2 import
  typos and spaces
  fixed typos in Rd files
  readMSnSet2 now also accepts a data.frame as input
  no empty new line
  new devel version
  Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by meowcat)
  remove spurious call to browser
  note on sort(i) in pSet,[
  fix missing paren
  feature names testing
  new sampleNames<- for pSet/MSnExp objects
  new devel version
  bump version and update NEWS to document latest PRs
  change spectrum order to natural sorting (add missing MS2 level); #69
  change spectrum order to natural sorting
  upate style
  update news
  rewrite featureCV
  add colSd to calculate sd column-wise
  ...

From: Laurent <[email protected]>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@113063 bc3139a8-67e5-0310-9ffc-ced21a209358
lgatto pushed a commit that referenced this issue Sep 7, 2017
Merge branch 'master' into devel
59f214d 
* master:
  Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by meowcat)
  remove spurious call to browser
  note on sort(i) in pSet,[
  fix missing paren
  feature names testing
  new sampleNames<- for pSet/MSnExp objects
  new devel version

From: Laurent <[email protected]>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@111609 bc3139a8-67e5-0310-9ffc-ced21a209358
lgatto pushed a commit that referenced this issue Sep 7, 2017
Merge branch 'master' into devel
761a004 
* master: (860 commits)
  selective ggplot2 import
  typos and spaces
  fixed typos in Rd files
  readMSnSet2 now also accepts a data.frame as input
  no empty new line
  new devel version
  Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by meowcat)
  remove spurious call to browser
  note on sort(i) in pSet,[
  fix missing paren
  feature names testing
  new sampleNames<- for pSet/MSnExp objects
  new devel version
  bump version and update NEWS to document latest PRs
  change spectrum order to natural sorting (add missing MS2 level); #69
  change spectrum order to natural sorting
  upate style
  update news
  rewrite featureCV
  add colSd to calculate sd column-wise
  ...

From: Laurent <[email protected]>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@113063 bc3139a8-67e5-0310-9ffc-ced21a209358
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@lgatto @meowcat