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Releases: choishingwan/PRSice

New Year Update: First Major Update of PRSice

08 Feb 22:17
@choishingwan choishingwan
2.1.0.beta
9460114
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New Year Update: First Major Update of PRSice Pre-release
Pre-release

Description

This is the first ever major update of PRSice 2 where there are a number of changes made where some of the old command line options are changed (e.g. --cov-header is now depreciated and replaced by --cov-col for consistency)

Below are the detail log of the changes made

Update Info

  1. Clumping algorithm has been completely changed. We should no longer encounter memory problem without receiving a meaningful error message. We have also replace most of our clumping code with the PLINK algorithm
  2. Original --score option is now renamed to --missing to better resemble it's core function (as in how to interpret missing score)
  3. --score option is now used to determine which kind of PRS to be calculated, (averaging (default), sum only or standardise)
  4. PRSice now support gz file as base
  5. Fix some problems related to the reference LD panel
  6. --all is now named as --all-score for better clarity
  7. We changed the default behaviour of PRSice to always include the p-value threshold of 1. Therefore we replace --full with --no-full to account for this change.
  8. Introducing the --no-default flag. This will forbid PRSice from guessing the data field from the base file. So for example, the BP column will not be included if user use the --no-default flag and didn't provide the --bp BP option
  9. Introducing the --maf, --geno, --info, --ld-maf, --ld-geno and --ld-info flag which allow direct genotyping QC to be performed on the target data (NOTE: We have only test run these flags on the binary plink format. So it would be nice if user help us to test run these for the bgen file)
  10. You can now filter SNPs from the base file using the --info-base and --maf-base option
  11. PRSice now comes with a window version. To enable that, a number of changes have been made:
    1. pthread instead of std::thread is used.
    2. Replace p-value calculation code with PLINK codes and remove boost library. P-value calculated will be slightly different when compared to previous versions though the difference only occur at very small precision level, therefore should not affect the interpretation of data.
  12. Replace --cov-header by --cov-header for consistency (w.r.t --pheno-col)

Update (14/2/2018)

  1. Fix problem with --ld where when sample size of the reference and target is different, the clumping algorithm goes wrong
  2. Fix PRS calculation, now all score should systematically be 2 times the score generated before (because of not multiply the score by ploidy), this will have no effect on the R2 and p-value calculated

Update (8/2/2018)

  1. Fix problem with PRSet PRS where PRS does not clear out for new pathways
    Note: Permutation for PRSet might still have memory error, we are currently trying to handle that

Update (26/1/2018)

  1. Fix memory problem with permutation (now we assume less memory are available, 1gb vs 10gb)
  2. Fix problem with seed not set

Update (25/1/2018)

  1. Fix problem with permutation
Assets 9
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Support for Different Genetic Models

27 Oct 12:27
@choishingwan choishingwan
2.0.14.beta
ca8c3b7
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Support for Different Genetic Models Pre-release
Pre-release

Update Log

  • Now support different genetic models, including:
    • add - Additive model, code as 0/1/2 (default)
    • dom - Dominant model, code as 0/1/1
    • rec - Recessive model, code as 0/0/1
    • het - Heterozygous only model, code as 0/1/0
  • Removed some of the unused functions
  • Fix bug with permutation
  • Add in fall back when ggplot or data.table cannot be install
    • Will try to use the base graphics from R to draw the plots
      • (Plots will have uglier legend when compared to those drawn by ggplot)

Bug fix

  • Solved problem with BGEN file where PRSice didn't generate the list of valid SNPs
  • Solved problem where the log file sometimes missed some error messages

20171109

  • Fix problem with quantile plot error bar
  • Can now directly execute the Rscript without using the Rscript call

20171111

  • Fix problem when handling strand flipping for bgen file format

20171116

  • Fix problem where PRSice doesn't allow no phenotype when using --no-regress
  • Fix problem with keep-ambig
  • Note: Due to my slow internet, I am not able to include the TOY dataset in this zip file
Assets 10
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Memory Fix

14 Oct 01:42
@choishingwan choishingwan
2.0.13.beta
bdbab85
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Memory Fix Pre-release
Pre-release

Update Log

  • Reduce memory usage, therefore reducing change of seeing the error message: Terminated something something uncaught exception
  • Add PRSet and multi-target phenotype output graph
  • Reorganize code such the PRSet will run slower but more memory efficient
  • Add in fall back when data.table or ggplot2 cannot be install

Quick Bug fix

  • log file name was not defined before seed output
Assets 5
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