RelateAdmix: Difference between revisions
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<pre> | <pre> | ||
?relate | ?relate | ||
</pre> | |||
== Run example using C == | |||
After installing the program you can try running it on the example data set in the data folder. If you are in the | |||
src folder where you installed relateAdmix and you have the software Admixture installed this can be done by typing | |||
<pre> | |||
cd ../data | |||
admixture smallPlink.bed 2 | |||
../src/relateAdmix -plink smallPlink -f smallPlink.2.P -q smallPlink.2.Q -P 20 | |||
</pre> | </pre> | ||
Revision as of 13:30, 21 August 2013
Software for inferring relatedness even if the individuals are admixed. To infer the relatedness you will need to known the individuals admixture proportions and the allele frequencies in each of the possible populations. This can be done e.g. using the program Admixture.
Installation
Download
Installation of R package
wget http://www.popgen.dk/software/download/relateAdmix/relateAdmix_0.05.tar.gz R CMD INSTALL relateAdmix_0.05.tar.gz
Installation of C program
wget http://www.popgen.dk/software/download/relateAdmix/relateAdmix_0.05.tar.gz tar -xvzf relateAdmix_0.05.tar.gz cd relateAdmix/src/ mv CPP_Makefile Makefile make
Run example
Run example using R
After installing the package you can load it into R and try the example
library(relateAdmix) example(relate)
This shows an example of how to use the package. More information can be found in the man pages
?relate
Run example using C
After installing the program you can try running it on the example data set in the data folder. If you are in the src folder where you installed relateAdmix and you have the software Admixture installed this can be done by typing
cd ../data admixture smallPlink.bed 2 ../src/relateAdmix -plink smallPlink -f smallPlink.2.P -q smallPlink.2.Q -P 20