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Package Updates.txt
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Package Updates.txt
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Package Updates
10/25/2018
- POEx option is now working
- NOEx (negative odd electron assignment) has now been implemented
- Fluorine assignment now implemented (Flx)
01/18/2019
- See documentation for more in depth description of the changes
- Addition of more versions of MFAssign functions (MFAssignAll_MSMS, MFAssign_RMD, MFAssignCHO_RMD)
- Added new noise estimation function "KMDNoise" and renamed original to "HistNoise"
- Included 34S and 2 13C as potential isotopic masses in IsoFiltR
- Improved mass recalibration by adding a segmented "walking" component
- Changed name of MFRecalcheck to "Recal"
- Changed name of MFRecalList to "RecalList"
- Added second mass recalibration function "Recal_2", which is slightly different than "Recal"
- Generally enhanced performance and speed of the functions in the package
- Improved molecular formula assignment by decreasing incorrect sulfur assignments
05/13/2019
- Made the sulfur isotope check optional via the "SulfCheck" parameter
- Removed MFAssignAll() and MFAssignAll_MSMS()
- Added the functionality of those functions to MFAssign and MFAssignCHO() with the parameters "Ambig" and "MSMS" respectively
- Added RecalX() and Recal_2X() as additional recalibration functions. See documentation for more information
- General improvements to flexibility and transparency of moleular formula assignment.
10/10/2019
- Combined all four versions of Recal() into a single function. All functionality is still available, but is accessed via the "opt" parameter in the function. opt = 1 replaces RecalX(), opt = 2 replaces Recal_2X(), opt = 3 replaces Recal(), and opt = 4 replaces Recal_2().
- Additional controls were added to IsoFiltR() so now the user can set the matching error allowance for mono/iso pairs using the "Carberr" or "Sulferr" parameters. The maximum allowed 34S ratio can also be set by the user now using the "Sulfrat" parameter.
- Internal change to MFAssign() and MFAssignCHO() now check the O/C and H/C ratios during formula extension, if they exceed the limits set by the user, the formula is discarded. This was done post formula extension in previous versions.
01/27/2020 (Version 1.0.0)
Please see the ReadMe for more information about changes to the code.
- Improvements to formula extension methodology for improved formula assignment
- Reworked and simplified recalibration in the Recal() function
- Increased user control of "slice" in KMDNoise()
- Improved isotope identification and assignment through changes in IsoFilter() and MFAssign()/MFAssignCHO()
- Made the N3OS to 13C correction in MFAssign() optional
08/14/2020 (Version 1.0.1)
- "Under the hood" changes to allow the package to work with the changes made in R version 4.0.0 and greater.
- Previous version has been archived to create a record of the version of code described in the publication:
Schum SK, LE Brown, LR Mazzoleni, MFAssignR: Molecular Formula Assignment Software for Ultrahigh Resolution Mass Spectrometry
Analysis of Environmental Complex Mixtures, in press, Environmental Research, 2020.
- New elements have been added for assignment, including 79Br, 81Br, and 126I.
- All functions have been adjusted so that they can handle a two or three column data frame, allowing the user to assign molecular formulas to LC-MS data while retaining the retention time.
- Made improvements to Recal() which allows it to avoid the problems associated with having "holes" in the calibration mass list, which caused errors previously.
- Made improvements to FindCoreFormula() which improve the assignment coverage from the initial CHOFIT assignment, which improves the assignment of isolated peaks.
- Made general improvements to IsoFiltR to ensure all appropriate peaks are retained.
08/17/2020 (Version 1.0.1)
- Fixed an error in IsoFiltR which caused two column data frames not to work properly. Now IsoFiltR should work for both 2 and 3 column data frames as intended.
- Fixed a error that caused MFAssignCHO and MFAssignCHO_RMD to run slower than they should.
08/21/2020 (Version 1.0.1)
- Fixed an error in IsoFiltR which was causing part of the "Iso" output to be populated with NAs.
- Fixed an error in MFAssign and MFAssign_RMD that incorrectly classified a single formula as ambiguous, when it was unambiguous.
09/28/2020 (Version 1.0.1)
- Fixed a mis-labeled column in the "RecalList" output of the Recal function. Now it will properly be labeled as "abundance" instead of "exp_mass"
- Also changed "Exp_mass" to "exp_mass" in the "RecalList" output.
- Fixed an issue in MFAssign and MFAssign_RMD where the output plots would indicate the presence of a single ambiguous formula, when none were actually present.
02/09/2021 (Version 1.0.1)
- Fixed a problem with IsoFiltR() that led to an error when no matches of a specific isotope pair were found.
06/01/2021 (Version 1.0.1)
- Fixed a problem where NMScut = "off" could cause an error in the molecular formula assignment functions.
08/31/2021 (Version 1.0.1)
- Fixed a problem where fluorine and NH4+ adducts did not assign correctly.
- "Formula Assignment Markdown Example.RMD" was added to Supplemental MFAssign Scripts. This markdown provides an example of molecular formula assignment
using MFAssignR and the packages that need to be installed to use MFAssignR.
06/16/2022 (Version 1.0.2)
- Fixed issues that caused MFAssign, MFAssign_RMD, MFAssignCHO, and MFAssignCHO_RMD to have errors in R version 4.2.0.
- Fixed a minor issue that caused formula groups to be represented on the VK and MZGroups plots that were not present in the actual dataset. This addresses a purely visual issue and has no other impacts on the data output.
04/12/2023 (Version 1.0.2)
- Fixed an issue that could generate warnings when running MFAssign, MFAssign_RMD, MFAssignCHO, and MFAssignCHO_RMD. It also had a reported impact on performance.
Thank you to the users for bringing the issue to my attention.
05/25/2023 (Version 1.0.2)
- Fixed an issue with IsoFiltR that occasionally caused and error regarding the lack of precision when converting between integer and double. This was addressed by "wrapping" Sect and Over with ceiling() when those numbers are first defined.