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artMS v1.10.2

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@biodavidjm biodavidjm released this 14 Jul 07:30
· 4 commits to master since this release
v1.10.2
c06d859

Changes in version 1.10.2 (2021-07-13)

  • Bug fix affecting {artmsAnalysisQuantifications()}
  • Allow {artmsAnalysisQuantifications()} to process previous versions of artMS
  • Change Extension of {artms_sessionInfo_quantification} file from {.txt} to {.log}
  • New parameters available in {artmsQuantification()}, including:
    • Parameter {printTables}. Default {TRUE}, prints tables. FALSE otherwise.
    • Parameter {return_results_object}. If TRUE, it returns a list of data frames with MSstats results. Default is FALSE
    • If both {printTables} and {printPDF} are FALSE, then {return_results_object} becames TRUE and a list of data frames is returned
  • Change default parameters of the configuration files: less verbose

Changes in version 1.10.1 (2021-06-30)

  • Addressing major changes in MSstats
    • R version larger than 4.1 is now required
    • Fractions: the option "Fractions" is removed from the configuration file. If fractions are present, the user must include a "Fraction" column in the keys.txt file, which artMS will detect automatically.
    • {artmsQualityControlEvidenceBasic}: fraction parameter no longer required (automatically detected from the keys file)
    • {keys.txt}: use {Fraction} instead of {FractionKey}
  • External packages used exclusively by the {artmsAnalysisQuantifications} function are not required. Those packages will have to be installed before running this function.
  • {artmsAvgIntensityRT}: argument {species} is not longer required
  • Example datasets:
    • {artms_data_ph_evidence}: the size has been significantly reduced (bioconductor requirement). Only two biological replicates and 1/20 of the lines selected randomly. Including only 36 columns from the original evidence file
    • {artms_data_ph_msstats_results}: output from running {artmsQuantification} on the full version of the evidence file, including 4 biological replicates (instead of the reduced version available in the package)
    • {artms_data_ph_msstats_modelqc}: output from running {artmsQuantification} on the full version of the evidence file, including 4 biological replicates (instead of the reduced version available in the package)
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