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v0.9.0 (CRAN release)

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@ethanbass ethanbass released this 31 May 15:48
· 11 commits to master since this release
v0.9.0
6884128

chromConverter 0.9.0

Breaking changes

  • Consolidated sample_id and vial metadata fields into new sample_position field.
  • Added sparse argument for rainbow parser (now enabled by default) to remove zeros form long-format MS data.
  • Changed order of what arguments in read_agilent_d to prioritize DAD data (instead of 2D chromatograms).
  • Fixed bug so that Varian long-format MS data is returned as a data.frame by default (rather than a matrix).
  • Added chrom_list class and print.chrom_list method. Instead of dumping the full contents of every chromatogram, prints a compact metadata summary with configurable columns (cols) and row limit (n).

New features

  • Added support for reading Agilent Common Analytical Markup Language (ACAML) files.
  • Added support for reading Agilent OpenLab method files (.amx).
  • Added preliminary support for reading "Chromatotec" .Chrom files through the read_chromatotec function.
  • Added support for reading regular utf8-encoded csv files.
  • Pass source file through when reading agilent_dx files so that the original source file is stored in metadata instead of a temp file.
  • Added warning in read_chroms for duplicated names as they may silently interfere with downstream analyses.

Improved support for exporting files

  • Added option to write ARW files in write_chroms. This format seems to be the simplest way to get DAD data into OpenChrom.
  • Added support for writing standard utf8-encoded csv files and fixed a bug causing column names to be prepended with "X".
  • Modified write_chroms so it invisibly returns file names of the exported chromatograms.
  • Improved error handling within write_chroms.

CDF

  • Fixed bug causing failure to write chromatograms with missing attributes to .cdf (thanks to @pbulsink for PR #37).
  • Fixed bug causing failure to write existing timestamp data to .cdf files.
  • Fixed bug causing failure to write ANDI chrom files on Windows due to failure to coerce numeric metadata to text.
  • Added additional metadata fields to exported CDF files.
  • Added additional test for writing CDF files with missing attributes.
  • Fixed CDF time range metadata bug.

mzML

  • Fixed write_mzml to correctly handle DAD spectra.
  • Added chromatograms to mzML files written by write_mzml.
  • Fixed incorrect CV accession for no compression (MS:1000576).

Other bug fixes and minor changes

  • Fixed entab parser so it translates .ch files to wide format when specified.
  • Fixed bug in read_agilent_d when subsetting data with the what argument.
  • Fixed Waters ARW parser so it can read files with missing metadata.
  • Added assumption that time units for data generated by rainbow parser are in minutes.
  • Rainbow parser now returns sparse MS data by default (excluding zeros) when long format is requested to match format returned by other parsers.
  • Fixed problems with Aston converters due to changes in reticulate behavior.
  • Fixed bug so that data from ANDI MS netCDF files can be returned as data.table object when specified by user.
  • Fixed 'Shimadzu' QGD bug affecting large values. Resolves (#44).
  • Fixed bug causing sample_position/vial metadata to be dropped when reading Agilent files.
  • Fixed bug so that temp directories created by certain file parsers (e.g., read_agilent_dx and read_themoraw) are actually deleted on completion.
  • Refactored extract_metadata function for simplicity.

Contributors

pbulsink
Assets 2
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