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[[Category:Software]]
[[Category:Software]]
= Overview =
= Overview =
A few rare variants tests (Li-Leal's CMC and Madsen-Browning's weighted method) are implemented in the logisitc regression framework using C++.
'''(See [[http://zhanxw.github.io/rvtests rvtests]] for more powerful rare-variant association test software and/or preparation for meta-analysis)'''
A few rare variants tests (Li-Leal's CMC and Madsen-Browning's weighted method) are implemented in the logisitc regression framework using C++. Please contact Youna Hu (youna@umich.edu) for comments, suggestions or questions.
The source code is located at [[File:RV3Tests.v1.tar]]
The source code is located at [[File:RV3Tests.v1.tar]]
You can just download the tar file, extract it and go to the RV3Test.v1 folder to type make all to compile the code, the binary file will then be in the exectuables folder.
You can just download the tar file, extract it and go to the RV3Test.v1 folder and type make all to compile the code, the binary file will then be in the exectuables folder.
= Example =
= Example =
;--genofile: A genotype 012 matrix (.012 is the file) This file can be prepared by using the prepare012s
;--genofile: A genotype 012 matrix (.012 is the file) This file can be prepared by using the prepare012s
source code [[File:vcfReader.v1.tar]]
source code [[File:vcfReader.v1.tar]]
Again, extract the tar file and then go into the directory to type make all to compile the code, you then will find binary file in the executables folder.
Again, extract the tar file and then go into the directory to type make all to compile the code,
you then will find binary file in the executables folder.
Note: You should use Yanming's vcf annotation [http://genome.sph.umich.edu/wiki/VcfCodingSnps] on your vcf file first to output a annotated vcf file. You SHOULD record the log file, which will be later used to define the gene list.
Note: You should use Yanming's vcf annotation [http://genome.sph.umich.edu/wiki/VcfCodingSnps] on your vcf file first
to output a annotated vcf file. You SHOULD keep the log file from the annotation, which will be used to create the gene list.
Data File PREPARATION
Data File PREPARATION
