2,004
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Single Variant Analysis
===Single Variant Analysis===
===Single Variant Analysis===
The following command lines let you run single variant association analysis of trait "LDL" using score test, after inverse normalization of the quantitative trait and adjusting covariates. --traitName specifies the single trait or traits you want to analyze in this batch. If this option is not used, then all traits coded in data file will be analyzed accordingly. --SingleVarLRT provides essentially the same test as in merlin --fastAssoc option.
The following command lines let you run single variant association analysis of trait "LDL" using score test, after inverse normalization of the quantitative trait and adjusting covariates. --traitName specifies the single trait or traits you want to analyze in this batch. If this option is not used, then all traits coded in data file will be analyzed accordingly. --SingleVarLRT provides essentially the same test as in merlin --fastAssoc option.
./famrvtest -p your.ped -d your.dat --vcf your.vcf.gz --SingleVarScore --inverseNormal --useCovariates --traitName LDL
./famrvtest --ped your.ped --dat your.dat --vcf your.vcf.gz --SingleVarScore --inverseNormal --useCovariates --traitName LDL
Futhermore, if you want to run likelihood ratio test and wald test at the same time, the following command should do the work:
Futhermore, if you want to run likelihood ratio test and wald test at the same time, the following command should do the work:
./famrvtest -p your.ped -d your.dat --SingleVarScore --SingleVarLRT --SingleVarWald --inverseNormal --useCovariates --traitName LDL
./famrvtest --ped your.ped --dat your.dat --SingleVarScore --SingleVarLRT --SingleVarWald --inverseNormal --useCovariates --traitName LDL
All the above commands will let you do family-based association analysis using kinship matrices generated using pedigree structure coded in pedigree file. The following command lines show examples of using genotype to estimate empirical relationship matrix to do the work.
All the above commands will let you do family-based association analysis using kinship matrices generated using pedigree structure coded in pedigree file. The following command lines show examples of using genotype to estimate empirical relationship matrix to do the work.
./famrvtest -p your.ped -d your.dat --SingleVarScore --SingleVarLRT --SingleVarWald --inverseNormal --useCovariates --traitName LDL --kinGeno
./famrvtest --ped your.ped --dat your.dat --SingleVarScore --SingleVarLRT --SingleVarWald --inverseNormal --useCovariates --traitName LDL --kinGeno
===Gene-level Association===
===Gene-level Association===
