Pipeline for GWAS Using MLMM

Pipeline for Genome-Wide Association Study using Multi-Locus Mixed Model from Segura V, Vilhjálmsson BJ et al. (2012) . The pipeline include detection of associated SNPs with MLMM, model selection by lowest eBIC and p-value threshold, estimation of the effects of the SNPs in the selected model and graphical functions.


mlmm.gwas v1.0.2 (2018/03/28)

Initial release on CRAN

mlmm.gwas v1.0.3 (2018/05/03, Olivier Guillaume)

  • Correction of a bug in eBIC_allmodels with FM or FMI models.
  • Correction of a bug in the manhattan.plot function.
  • R3.5 support

mlmm.gwas v1.0.4 (2018/07/18, Olivier Guillaume and Alexandra Duhnen)

Important changes (bug correction and changes of functionality):

  • BLUE estimation in Estimation_allmodels have been modified for more coherence, with same constraints for all effects (AD)
  • Correction of a bug in the genotypes.boxplot function, the tukey classes symbols were wrong in some cases (OG)
  • Correction of a bug in the run_entire_gwas_pipeline function, cofactors were not used for effects estimation (AD)
  • The package dependency is now R (>= 3.3.0) instead of R (>= 3.4.0).

Minor changes:

  • Chromosome are now ordered in alphanumerical order in Manhattan plot instead of alphabetical order (ie. 10 now comes after 9). (OG)
  • Special characters in marker names are now supported, especialy ":" that use to cause problem. (OG)
  • Unwanted graphical windows opened during mlmm_allmodels execution are now closed immediatly. The window is opened by the sommer:mmer2 function. A way to remove it entierely is yet to be found. (OG)
  • The marker order in the table generated by the Estimation_allmodels is now the same as the marker selection order in MLMM instead of alphabetical order (OG)
  • Correction of a small bug in the Estimation_allmodels function were underscore were injected in cofactor names (OG)

Reference manual

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1.0.6 by Clement Mabire, a year ago

Browse source code at https://github.com/cran/mlmm.gwas

Authors: Fanny Bonnafous [aut] , Alexandra Duhnen [aut] , Louise Gody [aut] , Olivier Guillaume[aut, cre] , Brigitte Mangin [aut] , Prune Pegot-Espagnet [aut] , Vincent Segura [aut] , Bjarni J. Vilhjalmsson [aut] , Clement Mabire [aut] , Timothee Flutre [aut]

Documentation:   PDF Manual  

GPL-3 license

Imports multcompView, multcomp, coxme, sommer, Matrix

Suggests knitr, rmarkdown

See at CRAN