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PATCHNOTES.md

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Patch notes

14-01-2021 (v0.5.1)
  • Fixed issue with MAF calculation in .gwama()
04-01-2021 (v0.5.0)
  • Please update to this version! Merging and meta analyses did not work properly in previous versions.
  • For now using MergedSumStats.meta_analyze() will instead run .gwama() with an identity matrix (functionally identical to .meta_analyze(method='ivw')), as this appears to work reliably.
30-11-2020 (v0.4.6)
  • Fix: Merge using a list of SumStats now propagates arguments properly
  • Fix: Meta analyzing now properly sums N across all summary statistics
  • Fix: Fixed an issue that would prevent proper outer merge
30-11-2020 (v0.4.5)
  • Fix: Merge using a list of SumStats now propagates arguments properly
  • Fix: Meta analyzing now properly sums N across all summary statistics
16-09-2020 (v0.4.4)
  • Bugfix: Chromosome X now properly converted to 23
04-09-2020 (v0.4.3)
  • Bugfix: .describe() now returns min and max instead of min and min
  • Bugfix: .qc() now works with any column
28-07-2020 (v0.4.2)
  • Added an NotImplementedError when attempting to merge with low_memory and a method other than inner.
  • Added per_phenotype argument to .save() to save separate files for each phenotype in MergedSumStats objects.
  • Added phenotype argument to .save() to save file for a specific phenotype in MergedSumstats objects.
02-06-2020 (v0.4.1)
  • Fixed assertion issues that caused merging files and plotting merged files to fail.
15-05-2020 (v0.4)
  • Fixed export so that saving to a file with '.gz' extension now actaully gzips the output file.
  • Fixed data import to enable opening a pysumstats file saved as .pickle by initializing SumStats class. This will also check if the data is still stored when low_ram was set to True.
  • Merging sumstats now computes an overall MAF meta-analyzed sumstats can be reimported with pysumstats.
  • Added version number to SumStats objects.
  • Added kwargs to SumStats.qc for filtering on custom columns.
  • Added custom SumStats warnings. These warnings print always by default you can change this behavior with Pythons default warnings filter.
  • Reformatted documentation, now also includes a guide on opening and saving sumstats.
13-05-2020 (v0.3.1)
  • Fixed an issue where reading data would fail when values in n, bp, chr columns were NA. An attempt is now made to impute these values. If too many are missing a ValueError is thrown.
12-05-2020 (v0.3)
  • Added fig and ax arguments to pysumstats.plot.qqplot and pysumstats.plot.manhattan to enable plotting to existing figure and axis.
  • Added pysumstats.plot.pzplot, to visually compare Z-values from B/SE to Z-values calculated from the P-value.
  • Added pysumstats.plot.afplot, to plot allele frequency differences between summary statistics.
  • Added pysumstats.plot.zzplot, to plot differences in Z-values between summary statistics.
  • Added qqplot, manhattan, pzplot, afplot, zzplot functions to MergedSumStats object.
  • Added pzplot function to SumStats object.
  • Added plot_all functions to SumStats and MergedSumStats objects to automatically generate all possible plots for the object.
11-05-2020 (v0.2.3)
  • Fixed import errors and added manhattan and qq function to SumStats class
  • Added return statement to MergedSumStats.merge() when inplace=False and merging with other MergedSumstats.
  • Added docstrings to base, mergedsumstats, sumstats and utils.
  • Added docs
08-05-2020 (v0.2)
08-05-2020 (v0.1)
  • Adapted to be a package rather then a module.
  • Added low_ram argument to SumStats to read/write data to disk rather than RAM, in case of memory issues.