RelateAdmix - Revision history

Albrecht: /* Options */

2018-03-09T10:01:33Z

Options

← Older revision		Revision as of 12:01, 9 March 2018
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	; -plink [FILE]		; -plink [FILE]
	The binary plink file without postfix		The binary plink file without postfix
	; -f/-fname [FILE]		; -f/-fname [FILE]
	Ancestral population frequencies (e.g. estimated from ADMIXTURE with the .P filename		Ancestral population frequencies (e.g. estimated from ADMIXTURE with the .P filename

Albrecht: /* Options */

2018-03-09T10:01:14Z

Options

← Older revision		Revision as of 12:01, 9 March 2018
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	</pre>		</pre>

			; -plink [FILE]
			The binary plink file without postfix
			; -f/-fname [FILE]
			Ancestral population frequencies (e.g. estimated from ADMIXTURE with the .P filename
			; -q/-qname [FILE]
			Ancestral admxiture proportions (e.g. estimated from ADMIXTURE with the .Q filename
			; -o [NAME]
			Output filename
			; -P [INTEGER]
			Number of threads (not implemented for inbreeding)
			; -F [0 or 1]
			Use -F 1 if you want to estimate the inbreeding coefficient instead of relatedness

	=== Output file format===		=== Output file format===

Albrecht: /* Run example using C */

2018-03-09T09:56:09Z

Run example using C

← Older revision		Revision as of 11:56, 9 March 2018
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	== Run example ~~using C~~ ==		== Run example from terminal ==

	After installing the program you can try running it on the example data set in the data folder,		After installing the C version of the program you can try running it on the example data set in the data folder,
	which consists of 50 individuals that are admixed from 2 source populations.		which consists of 104290 SNP for 126 individuals that are admixed from 2 source populations.

	If you are in the src folder where you installed relateAdmix and you have the software [http://www.genetics.ucla.edu/software/admixture/ ADMIXTURE] installed this can be done as follows:		If you are in the src folder where you installed relateAdmix and you have the software [http://www.genetics.ucla.edu/software/admixture/ ADMIXTURE] installed this can be done as follows:
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	</pre>		</pre>
	[[File:relAd.png\|thumb]]		[[File:relAd.png\|thumb]]


			=== Options ===
			see options by running with out additional arguments:
			<pre>
			../src/relateAdmix
			Arguments:
			-plink name of the binary plink file (excluding the .bed)
			-fname Ancestral population frequencies
			-qname Admixture proportions
			-o name of the output file
			Setup:
			-P Number of threads
			-F 1 if you want to estimate inbreeding

			</pre>

Albrecht: /* Citing and references */

2018-02-22T14:57:55Z

Citing and references

← Older revision		Revision as of 16:57, 22 February 2018
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	[http://www.ncbi.nlm.nih.gov/entrez?Db=pubmed&Cmd=ShowDetailView&uid=24215025 pubmed]		[http://www.ncbi.nlm.nih.gov/entrez?Db=pubmed&Cmd=ShowDetailView&uid=24215025 pubmed]
	[http://www.bioinformatics.org/texmed/cgi-bin/list.cgi?PMID=24215025 bibtex]		[http://www.bioinformatics.org/texmed/cgi-bin/list.cgi?PMID=24215025 bibtex]


			=== Inbreeding ===

			The model used for inbreeding is described in
			Ida Moltke, Matteo Fumagalli, Thorfinn S Korneliussen, Jacob E Crawford, Peter Bjerregaard, Marit E Jørgensen, Niels Grarup, Hans Christian Gulløv, Allan Linneberg, Oluf Pedersen, Torben Hansen, Rasmus Nielsen, Anders Albrechtsen
			Uncovering the genetic history of the present-day Greenlandic population.
			Am. J. Hum. Genet.: 2015, 96(1);54-69
			[https://www.sciencedirect.com/science/article/pii/S0002929714004789?via%3Dihub Article]

	=== ADMIXTURE ===		=== ADMIXTURE ===
	D.H. Alexander, J. Novembre, and K. Lange. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655–1664, 2009.		D.H. Alexander, J. Novembre, and K. Lange. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655–1664, 2009.


	= change log =		= change log =

Albrecht at 14:55, 22 February 2018

2018-02-22T14:55:21Z

← Older revision		Revision as of 16:55, 22 February 2018
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	=Brief description=		=Brief description=
	This page contains information about the program called relateAdmix, which can be used to infer relatedness coefficients for pairs of individuals even if they are admixed. The program has both an R interface and a C interface. Below is a description of how to install and use each of them. To be able to infer the relatedness you will need to know the individuals admixture proportions and the allele frequencies in each of the possible populations. This can be done e.g. using the program [http://www.genetics.ucla.edu/software/admixture/ ADMIXTURE] as shown in the example of how to use the C interface.		This page contains information about the program called relateAdmix, which can be used to infer relatedness coefficients for pairs of individuals or inbreeding coefficients even if they are admixed. The program has both an R interface and a C interface. Below is a description of how to install and use each of them. To be able to infer the relatedness you will need to know the individuals admixture proportions and the allele frequencies in each of the possible populations. This can be done e.g. using the program [http://www.genetics.ucla.edu/software/admixture/ ADMIXTURE] as shown in the example of how to use the C interface.

	=Installation - Linux/MAC=		=Installation - Linux/MAC=

Albrecht: /* Installation of C/C++ program */

2017-08-04T07:18:27Z

Installation of C/C++ program

← Older revision		Revision as of 09:18, 4 August 2017
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	git clone https://github.com/aalbrechtsen/relateAdmix.git		git clone https://github.com/aalbrechtsen/relateAdmix.git
	cd relateAdmix/src		cd relateAdmix/src
	mv CPP_Makefile Makefile		cp CPP_Makefile Makefile
	make		make
	</pre>		</pre>

Albrecht: /* Installation of C/C++ program */

2017-08-04T07:17:30Z

Installation of C/C++ program

← Older revision		Revision as of 09:17, 4 August 2017
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	<pre>		<pre>
	git clone https://github.com/aalbrechtsen/relateAdmix.git		git clone https://github.com/aalbrechtsen/relateAdmix.git
	cd relateAdmix/~~scr~~		cd relateAdmix/src
	mv CPP_Makefile Makefile		mv CPP_Makefile Makefile
	make		make

Albrecht: /* Installation of R package */

2017-07-14T09:29:42Z

Installation of R package

← Older revision		Revision as of 11:29, 14 July 2017
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	install_github("aalbrechtsen/relateAdmix")		install_github("aalbrechtsen/relateAdmix")
	</pre>		</pre>

			Or install from the command line


	<pre>		<pre>

Albrecht: /* Installation of R package */

2017-07-14T09:05:57Z

Installation of R package

← Older revision		Revision as of 11:05, 14 July 2017
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	<pre>		<pre>
	git clone https://github.com/aalbrechtsen/relateAdmix.git		git clone https://github.com/aalbrechtsen/relateAdmix.git
	R CMD ~~build~~ relateAdmix		R CMD INSTALL relateAdmix
	</pre>		</pre>

Albrecht at 08:35, 14 July 2017

2017-07-14T08:35:41Z

← Older revision		Revision as of 10:35, 14 July 2017
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	== Installation of R package ==		== Installation of R package ==

			If you have the devtools packages (https://github.com/hadley/devtools) installed in R then you can install the package i R directly from github

	<pre>		<pre>
	~~wget http://www.popgen.dk/software/download~~/relateAdmix~~/relateAdmix_0.14.tar.gz~~		library(devtools)
	~~R CMD INSTALL relateAdmix_0.14.tar.gz~~		install_github("aalbrechtsen/relateAdmix")
	</pre>		</pre>

	~~MAC user might have to use curl instead of wget~~		<pre>
			git clone https://github.com/aalbrechtsen/relateAdmix.git
			R CMD build relateAdmix
			</pre>

			or build and install
			<pre>
			git clone https://github.com/aalbrechtsen/relateAdmix.git
			R CMD build relate
			R CMD INSTALL Relate_<add version number>.tar.gz
			</pre>

	=== Problems with zlib ===		=== Problems with zlib ===
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	<pre>		<pre>
	~~tar -xf relateAdmix_0.14.tar.gz~~
	rm relateAdmix/src/Cinterface.*		rm relateAdmix/src/Cinterface.*
	rm relateAdmix/src/Makefile #only needed if you compiled the C program		rm relateAdmix/src/Makefile #only needed if you compiled the C program
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	</pre>		</pre>

	== Installation of C program ==		== Installation of C/C++ program ==
	<pre>		<pre>
	~~wget http~~://~~www~~.~~popgen.dk~~/~~software/download~~/relateAdmix~~/relateAdmix_0.14.tar~~.gz		git clone https://github.com/aalbrechtsen/relateAdmix.git
	~~tar -xvzf relateAdmix_0.14.tar.gz~~		cd relateAdmix/scr
	cd relateAdmix/~~src/~~
	mv CPP_Makefile Makefile		mv CPP_Makefile Makefile
	make		make