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The following command lines let you run gene-level association analysis of genes listed in "your.genes.groupfile" for trait "LDL" using SKAT, Madsen-Browning weighted burden, rare allele counts un-weighted burden and collapsing burden and variable threshold tests, after inverse normalization of the quantitative trait and adjusting covariates. Only rare variants with maf less than or equal to 0.05 and minor allele count greater than or equal to 3 are grouped.
The following command lines let you run gene-level association analysis of genes listed in "your.genes.groupfile" for trait "LDL" using SKAT, Madsen-Browning weighted burden, rare allele counts un-weighted burden and collapsing burden and variable threshold tests, after inverse normalization of the quantitative trait and adjusting covariates. Only rare variants with maf less than or equal to 0.05 and minor allele count greater than or equal to 3 are grouped.
./famRvTest -p your.ped -d your.dat --SKAT --MB --CMC_counts --CMC_binary --VTasymptotic --inverseNormal --useCovariates --traitName LDL --groupFile your.genes.groupfile --maxMaf 0.05 --mac 3
./famRvTest -p your.ped -d your.dat --SKAT --MB --CMC_counts --CMC_binary --VTasymptotic --inverseNormal --useCovariates --traitName LDL --groupFile your.genes.groupfile --maxMaf 0.05 --mac 3
== Change Log ==
* Released version 0.0.9 with a bug fixed for potential compiling error. (10/10/2013)
* Released version 2.0, a faster version and added single variant permutation test. (7/14/2014)
