NEWS

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flowPloidy 1.7.4 (2019-04-01)

User Visible Changes

• Note that the data files in 'flowPloidyData' are now accessed by functions, not variables. That is, instead of refering to the variable 'flowPloidyFiles', you now need to refer to the output of the function 'flowPloidyFiles()'. This was necessary to accomodate changes in the way R loads packages. This only effects the sample data from 'flowPloidyData', you should not change code referring to your own files.

flowPloidy 1.7.2 (2018-10-03)

WARNING

• There are some major user-visible changes in this version. The vignette has been updated, as have the manual pages. There may still be inconsistencies, please let me know if you find anything confusing. I still need to document the endopolyploidy workflow.

User Visible Changes

• Column names reported in tabulateFlowHist are completely revised. The new names should be self-explanatory, but will not match the column names reported in previous versions of flowPloidy. The output now includes the counts for the G1 and G2 peaks, as well as for each S-phase component.
• The browseFlowHist interface now has a "fail" button. This provides the user with the ability to reject a sample, even if flowPloidy can fit a model to it. For situations where flowPloidy succeeds in fitting a model to noise, or where only your standard is visible; selecting "fail" for these samples will guarantee that they show up as NAs in your summary data.
• The browseFlowHist interface now includes the option to add annotations. These are text comments, not part of the analysis. This allows the user to add notes such as "this sample needs to be rerun", or "exclude this, data is poor quality", etc.
• Analysis of endopolyploidy is supported by allowing the user to a) increase the number of peaks (samples) fit, up to a maximum of 6; b) to *not* fit G2 peaks (via the G2 = FALSE argument), so that the 2C, 4C, 6C etc peaks are all fit independently of each other, without requiring that the 4C peak be twice the size of the 2C peak; and c) reworking the output of tabulateFlowHist to allow for reporting the fit parameters for an arbitrary number of peaks.
• Internal changes to the model component code uncovered some bugs in the way G2 peaks were fit. These are fixed, and the model fitting works slightly better (higher success rate) as a consequence.

Internal Changes

• The G1, G2 and S-phase model components are now generated by helper functions. These allows me to tweak the component definitions in a single location, after which the change is automatically incorporated in all of the associated components.
• The above changes allowed me to replace a lot of duplicated code with more general forms, notably in the plotting and tabulating functions.
• Model parameters are now collected dynamically, so I don't need to hard-code the output of tabulateFlowHist. Parameters that the user won't need are indicated with the suffix 'P'; any parameter ending with 'P' is excluded from the output.
• Added a 'fail' slot to the FlowHist class, to support the fail button described above.

flowPloidy 1.5.6 (2018-03-08)

User Visible Changes

• BUG FIX: the G2 peak of the B sample was not getting incorporated into model construction, which caused model fitting to fail on samples with histograms skewed towards the left.
• Updated DebrisModel documentation.

Internal Changes

• Fixed broken test.

flowPloidy 1.5.3 (2018-01-17)

User Visible Changes

• The browser interface will no longer allow users to enter arbitrary text to select the number of samples. Only valid values, i.e., 1, 2, or 3, will be offered as choices. The old version would crash with a bad value for sample number.
• Improved file importing, so that low-quality samples for which peaks cannot be detected can still be imported.
• Added a new argument to FlowHist, so users can set the threshold below which the data is ignored when screening out debris. The default remains the same, 40, but users with very clean histograms, with peaks far to the left, can now lower this value if needed.
• Model fitting is now limited to the range of the data. That is, empty bins at the right (upper) end of the histogram will not be included when fitting the NLS. This addresses problems that generated inflated RCS values.
• The limits for the linearity parameter have been extended from 1.9-2.1, to 1.5-2.5. This will improve/enable model fitting on samples where the linearity (the ratio of the G2/G1 peaks) was outside the range 1.9-2.1.

flowPloidy 1.5.1 (2017-12-04)

Minor bug squashed

• Changes made upstream to ‘car::deltaMethod()' introduced a bug. This will be resolved as of 'car' version 2.1-7. Until that version of 'car' makes it’s way into CRAN, calling 'deltaMethod()' on an 'nls' object will require the argument 'vcov.' be explicitly set to 'vcov', a function in the stats package. This has been done in 'flowPloidy', and should be invisible to users. In addition, the bug is not present in the current R release, so it should not need to be backported to previous versions of flowPloidy.

flowPloidy 1.1.9 (2017-04-19)

User Visible Changes

• Users may now specify one or more internal standard sizes in functions FlowHist() and batchFlowHist(), via the argument 'standards'. These values will be presented to the user in the browseFlowHist() viewer, and after being set by the user, the value will be used to calculate the GC size in pg in the function tabulateFlowHist.
• Users may now select which peak in the histogram to treat as the internal standard when calculating GC values.
• New vignettes added: "Getting Started", and "Histogram Tour".
• Old vignette "overview" removed.
• Internal help pages greatly expanded, including many internal functions. See ?flowPloidy for an overview
• Many minor bug fixes and GUI tweaks (for browseFlowHist).

flowPloidy 1.1.3 (2016-11-25)

User Visible Changes

• Gating fully implemented in browseFlowHist! Major reorganization of the browseFlowHist layout.

flowPloidy 1.1.2 (2016-11-22)

User Visible Changes

• Added support for processing files with two standards present. A new argument is available for functions that load FCS files (batchFlowHist, FlowHist etc.): 'samples'. By default this is set to 2, to account for a single unknown and an co-chopped standard. If you are using two co-chopped standards (or really anytime you have three distinct samples chopped together), set samples = 3. This can also be changed interactively in the browseFlowHist GUI.
• The layout of the browseFlowHist GUI has been re-arranged somewhat to accomodate the new features mentioned above.
• The linearity flag is over-ridden when no G2 peaks are present. Without a G2 peak, linearity can't be properly fit. This leads to linear gradients, because the linearity parameter is used in the S-phase components.

flowPloidy 1.1.1 (2016-10-26)

Internal Changes

• Improved peak finding algorithm
• Reduced region searched for the starting bin for model fitting. Was originally 20, now set to 10. Need more data to establish best approach.

flowPloidy 0.99.3 (2016-10-17)

Internal Changes

• Updated DESCRIPTION to include URL and BugReports fields, mostly as an exercise to test SVN access and syncing SVN <-> git

flowPloidy 0.99.2 (2016-10-12)

Internal Changes

• added a new slot to ModelComponents, 'paramLimits', which allows lower and upper limits to be set for each model parameter. (corrects bug where linearity wanders below 1, giving nonsense results).
• rationalized the bounds of the data fit in the NLS procedure. Model fitting, and RCS calculation, are now all tied to the bin identified by fhStart. This selects the highest intensity (peak) in the first 20 non-zero channels, and ignores all channels below this point. Prior to this, the number of observations and associated degrees of freedom was calculated in an ad-hoc manner, making the RCS values (even-more) difficult to interpret; in addition, the single- and multi- cut values started at one channel, but the RCS calculations started on another channel, which didn't make sense.

flowPloidy 0.99.1 (2016-10-11)

User Visible Changes

• Vignette updated to include installation instructions for BioConductor

Internal Changes

• Added accessor functions for ModelComponent and FlowHist classes, so direct access of slots via the '@' operator is no longer used outside of the initialization functions.
• replaced some loops with vectorized calculations
• replaced call to 'eval' with a normal function call to 'nlsLM' in flowAnalyze.R.
• formatted NEWS file

flowPloidy 0.99.0 (2016-08-25)

• What's NEW? Everything so far!