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Releases: xiaolei-lab/rMVP

rMVP 1.0.4

01 Sep 10:09
@hyacz hyacz
1.0.4
94cb9c1
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rMVP 1.0.4 Latest
Latest

Enhance

  • adding Dockerfile
  • update README.md
  • update c++ for kinship computation

Bugfix

  • stop if hapmap major is not in 'ATGC'
  • fixed bug of skipping SNPs when converting vcf/hapmap to mvp genotype file format.
Assets 2
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rMVP 0.99.14.1

16 Jul 14:14
@hyacz hyacz
0.99.14.1
83b5fe1
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rMVP 0.99.14.1

Bug fix

  • Fixed an issue where workdir could not contain non-ASCII characters
  • Fixed an issue where matrix dimensions mismatch caused by adding SE output in the FarmCPU model
  • Fixed an issue where Windows could not overwrite bigmatrix due to file occupancy
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rMVP 0.99.14

12 Jul 15:58
@hyacz hyacz
0.99.14
63e7338
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rMVP 0.99.14

New features

  • Added Brent method as default variance component estimation method.
  • Output logs to disk by default.
  • Hapmap2MVP now supports single-letter encoding and parallel format conversion.
  • Added marker SE output.

Adjustment

  • SNP map suffix changed from ".map" to ".geno.map"
  • The strategy for computing PCs has been updated.
  • Speed mode and memory mode in the priority parameter are now only used to construct the kinship matrix.
  • Imputation in data format conversion does not generate intermediate files now.
  • Data format conversion now no longer generates PC and K by default.

Bug fix

  • !!! Fixed bug where SNP location was misaligned in multi-thread Bfile2MVP.
  • Fixed multithreading error caused by VECLIB on Microsoft R Open for macOS
  • replace mclapply with lapply on windows
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rMVP 0.99 Version build 13

12 Feb 04:05
@hyacz hyacz
0.99.13
0594261
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rMVP 0.99 Version build 13 Pre-release
Pre-release

In order to submit to Bioconductor, MVP is now renamed to rMVP and the version number is reset. In this version, MVP.Data is fully refactored in C++ and fixes several issues.

  • Unified installation package for Windows platform and Linux platform.
  • The 3D PCA map has been temporarily disabled, and we will improve this feature in subsequent versions.
  • Significantly reduced project size with Git LFS.
  • Add automatic tests.
  • MVP.Data update:
    • true NA support
    • rewrite by c++, faster
    • Provides some convenient functions
      • MVP.Data.VCF2MVP
      • MVP.Data.Bfile2MVP
      • MVP.Data.Hapmap2MVP
      • MVP.Data.Numeric2MVP
      • MVP.Data.Pheno
      • MVP.Data.Map
      • MVP.Data.PC
      • MVP.Data.Kin
      • MVP.Data.impute (beta)
      • MVP.Data.QC (beta)
  • remove bigpca, rfunctions
Assets 3
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