README.md

In andersgs/irelr: Pedigree Inference using Molecular Marker Data

Welcome

Welcome the R package irelr. This package provides functionality formerly available in the software iRel (Gonçalves da Silva and Russello 2011). It adds to the functionality by providing the user with additional relatedness indices to those in the original publication.

How to get it on Linux/Mac

I recommend installing the latest version of R from here. Then installing the latest version of RStudio from here.

You require Hadley Wickham's devtools package. From the R command prompt within RStudio, type:

install.packages('devtools')

Once that is complete, load devtools:

library(devtools)

You can then install irelr with the following command:

install_github("andersgs/irelr", build_vignettes = TRUE)

This might take a few moments as the vignette and source files are built.

How to get it on Windows

The latest release (version 0.0.6) has binaries available for R version 3.3.2.

To install:

1. Install dependencies: install.packages(c("adegenet","ape","data.table","ggplot2","gridExtra","hierfstat","moments","reshape2"))
2. Download the file
3. Open R, click on Packages -> Install package(s) from local files (If in RStudio select Tools -> Install Packages.. --- then select Install from: Package Archive File)
4. Select the file irelr_0.0.6_win.zip that you downloaded in step 1.

If all goes well, you should see the following message on the R command-prompt:

package irelr successsfully unpacked and MD5 sums checked

You should then be able to load irelr with the following:

library("irelr")

If all works out, you should see the following printed to the console:

Welcome to irelr (version 0.0.6)

How to use it

The package provides two main functions. A function to estimate relatedness indices from a set of genotypes, and a function to simulate indices under different relatedness categories.

The easiest way to get on your way with irelr is to have you data in a genepop format, with individual identifiers for each sample. irelr ignores population structure. The data file must have a .gen extension. To load your own genepop file:

library(adegenet)
file_path  <- "<path to file>/mydata.gen"
mydata <- read.genepop(file_path)

To estimate relatedness values:

library(adegenet)
data(nancycats)
irelr::estimate_rel(nancycats)

To simulate relatedness values for the available indices, one needs to define a k-vector (explained in the documentation and vignette). To simulated indices from 10,000 unrelated pairs:

library(adegenet)
data(nancycats)
irelr:sim_rel(nancycats, k_vector = c(1.0, 0.0, 0.0))

An extensive vignette is available with details on how to use the results from these two functions to reconstruct a pedigree. To access the vignette just type:

vignette(topic = 'use-irelr', package = 'irelr')

How to cite

Please cite the original iRel publication below, and this code specifically with the following:

References

Gonçalves da Silva A, Russello MA (2011) iRel: software for implementing pairwise relatedness estimators and evaluating their performance. Conservation Genetics Resources 3: 69-71. PDF

Updates

2017-01-29

• Added binary files for Windows for release 0.0.6 (built on version 3.3.2 of R) using win-builder.r-project.org
• Added instructions on how to install the Windows version

2015-12-05

• Updated the vignette to be compliant with the new version of Genind object taking advantage of the accessor functions.
• irelr now requires at least adegenet version 2.0.0
• Added a function read.genepop to replace the adegenet version 2.0.0 function which does not parse missing data correctly. The included version is a copy/paste of the function in the development version of adegenet found on here

License

irelr: an R package to reconstruct pedigrees from molecular data

Copyright (C) 2015 Anders Gonçalves da Silva and Michael A. Russello

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

andersgs/irelr documentation built on May 12, 2019, 2:41 a.m.