paramlink
Parametric Linkage and Other Pedigree Analysis in R
NOTE: 'PARAMLINK' HAS BEEN SUPERSEDED BY THE 'PEDSUITE' PACKAGES (< https://magnusdv.github.io/pedsuite/>). 'PARAMLINK' IS MAINTAINED ONLY FOR LEGACY PURPOSES AND SHOULD NOT BE USED IN NEW PROJECTS. A suite of tools for analysing pedigrees with marker data, including parametric linkage analysis, forensic computations, relatedness analysis and marker simulations. The core of the package is an implementation of the Elston-Stewart algorithm for pedigree likelihoods, extended to allow mutations as well as complex inbreeding. Features for linkage analysis include singlepoint LOD scores, power analysis, and multipoint analysis (the latter through a wrapper to the 'MERLIN' software). Forensic applications include exclusion probabilities, genotype distributions and conditional simulations. Data from the 'Familias' software can be imported and analysed in 'paramlink'. Finally, 'paramlink' offers many utility functions for creating, manipulating and plotting pedigrees with or without marker data (the actual plotting is done by the 'kinship2' package).
paramlink
The paramlink package has been superseded by the
pedsuite. In particular, the
main features of paramlink can now be found in the following packages:
- pedtools: Basic handling of pedigrees and marker data
- paramlink2: Parametric linkage analysis
- forrel: Forensic applications
- ribd: Relatedness coefficients and IBD triangle
Note that paramlink is not compatible with the pedsuite. It is
maintained only for legacy purposes and should not be used in new
projects.