PIXLRT is a package can be used for the analysis of(non pseudo-autosomal) SNPs on the X chromosome in case-parent triads.  The package can read genotypes in pedigree file format or matrices with number of minor allele copies for each of the mother, father, and affected offspring.  The parent-informed X chromosome likelihood ratio test (PIX-LRT) is then used to analyze the data. (Reference:  Wise A.S., et al   … 2014).



The following packages allow one to install PIXLRT into R.

For Windows users please download:
	PIXLRT_1.0.zip
The package can then be installed in R.  If you have not done this before, here are some brief instructions (these might vary with different versions of R):
1) Open R and click on "Packages->Install packages(s) from local zip files". 
2) Locate where you saved the .zip file and select that folder.  This should install the package. 
3) Inside your console load the package with "library(PIXLRT)". 

For UNIX or MAC users please download:
	PIXRLRT_1.0.tar.gz
The package can then be installed in R.  If you have not done this before, here are some brief instructions (these might vary with different versions of R):
1) Open R and click on "Packages & Data->Package Installer".
2) In the drop down menu in the upper right hand corner choose "Local Source Package" and the click "Install"
3) Find the folder where you download the .tar.gz file and open the .tar.gz file. This should install the package.
4) Inside your console load the package with "library(PIXLRT)" 

For specific questions on use of the functions, in R type "?PIX" and "?formatPed".