README.md

In zakrobinson/RSibPurge: A convenient R-interface for COLONY Version 2.0.6.5

RSibPurge

An R package that conveniently interfaces with COLONY Version 2.0.6.5 Executables (Mac & Linux). Executables are distributed freely, for noncommerical, educational purposes only.

Example RSibPurge workflow

devtools::install_github("zakrobinson/RSibPurge")

library(RSibPurge)

data("wgp_example")

create_params_colonyV2(projectname = "test1",offspring_alleles = wgp_example[,-1],geno = T,nCode = 2,likelihood = 0, RunLength = 1, precision = 0)

run_ColonyV2(colony_params = "test1_Colony_params.txt")

x<-read_colonyV2_BestFS(path = "test1.BestFSFamily")

purge_sibs(ids = x\$ID,fams = x\$FAMID,purge_to = 50,returnDF = T)

For more information on the program COLONY

Visit http://www.zsl.org/science/research-projects/software/

(1) Wang J. 2004. Sibship reconstruction from genetic data with typing errors. Genetics 166: 1963-1979.

(2) Wang J & Santure AW. 2009. Parentage and sibship inference from multi-locus genotype data under polygamy. Genetics 181:1579-1594.

(3) Jones OR & Wang J. 2010. COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources 10: 551-555.

(4) Wang J. 2012. Computationally efficient sibship and parentage assignment from multilocus marker data. Genetics 191: 183-194.

(5) Wang J. 2013. An improvement on the maximum likelihood reconstruction of pedigrees from marker data. Heredity 111: 165-174.

(6) Wang J. 2013. A simulation module in the computer program COLONY for sibship and parentage analysis. Molecular Ecology Resources 13: 734-739.

(7) Wang J & Scribner KT. 2014. Parentage and sibship inference from markers in polyploids. Molecular Ecology Resources 14: 541–553.

(8) Wang J. 2016. Individual identification from genetic marker data: developments and accuracy comparisons of methods. Molecular Ecology Resources 16: 163-175.

zakrobinson/RSibPurge documentation built on June 29, 2019, 3:19 a.m.