Software

Spmlficmcm R package

Authors: Moliere NGUILE-MAKAO and Alexandre BUREAU

The package SPmlficmcm implements the semiparametric maximum likelihood estimation method published by Chen et al., (2012) for the analysis of interaction effects involving genetic variants and environmental exposures on the risk of adverse obstetric and early-life outcomes. The main function of the package builds the nonlinear system from the database, uses the nleqsv function to resolve the nonlinear system, and estimates the coefficients and the standard errors from the log profile likelihood function with the one-step method. The modeling supposes that the distribution of maternal genotype and fetal satisfies the following assumptions: random mating , Hardy-Weinberg equilibrium and Mendelian inheritance. The package also permits to treat missing offspring genotype data.

Windows binary: SPmlficmcm_1.0.zip

Package source: SPmlficmcm_1.0.tar.gz

RVsharing R package

Authors: Alexandre BUREAU, Ingo RUCZINSKI and Samuel YOUNKIN

This R package computes the probability that a rare variant is shared by related subjects, given that the variant was observed in any of them. These probabilities are useful for the analysis of genomic sequencing data on related subjects. When the related subjects are affected by a disease, the probabilities are actually obtained under the null hypothesis of absence of genetic linkage and association of the variant to the disease. These probabilities quantify the extent to which the observed sharing of a rare variant is unlikely under the null hypothesis and are therefore p-values of a test of that null hypothesis. The package includes a function for the exact computation of the sharing probabilities in pedigrees without inbreeding and functions for approximating the probabilities using Monte Carlo simulation in inbred families and families whose founders are suspected to be related. The simulation functions also permit an evaluation of the sensitivity of the estimated probabilities to non-zero variant frequencies in the population, making possible the entry of more than one copy of the variant in the pedigree founders.

Windows binary: RVsharing_1.0.2.zip

Package source: RVsharing_1.0.2.tar.gz

LCAextend R package

Authors: Arafat TAYEB , Alexandre BUREAU and Aurélie LABBE

This R package performs a Latent Class Analysis of phenotypic measurements in pedigrees and a model selection based on one of two methods: likelihood-based cross-validation and Bayesian Information Criterion. It computes also individual and child-parents triplet class weights in a pedigree using an upward-downward algorithm. It takes into account the familial dependence defined by the pedigree structure by considering that a class of a child depends on his parents classes via triplet-transition probabilities of the classes. The package handles the case where measurements are available on all subjects and the case where measurements are available only on symptomatic (i.e. affected) subjects. Distributions for discrete (or ordinal) and continous data are currently implemented. The package can deal with missing data.

Windows binary: LCAextend_1.2.zip

Package source: LCAextend_1.2.tar.gz

Addrisk R package

This R package regroups various functions to estimate additive risk models and, for some functions, other types of risk models of a dichotomous outcome. It includes functions applying to prospective or cross-sectionnal cohort studies, functions designed specifically for nested case-control samples drawn from a cohort and functions for general sampling designs within cohorts. The lattter are restricted to having a single variable measured only in the sample, and that variable must be categorical with a small number of levels.

Windows binary: addrisk_1.0.zip

Package source: addrisk_1.0.tar.gz

HMM S-Plus/R module

Library of S-Plus/R functions to fit continuous time hidden Markov models. Based on an earlier FORTRAN program written by James P. Hughes. It is still a beta version.
S-Plus: module and  Installation instructions.
R: module.

Plasmin

A software package that I developed to apply MCMC methods to multilocus linkage analysis on large pedigrees. This one too is in beta version.
Download Plasmin.

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Last updated 2013/10/25