Changes

== Input Files ==

== Input Files ==

famRvTest needs the following files as input: PED and DAT file in Merlin format, '''AND/OR''' a VCF file. When genotypes are stored in PED and DAT file, the VCF file is not needed. However, even if genotypes are saved in a VCF file, PED and DAT files are still needed for carrying covariate and trait information.  

famrvtest needs the following files as input: PED and DAT file in Merlin format, '''AND/OR''' a VCF file. When genotypes are stored in PED and DAT file, the VCF file is not needed. However, even if genotypes are saved in a VCF file, PED and DAT files are still needed for carrying covariate and trait information.  

=== PED and DAT Files ===

=== PED and DAT Files ===

* When PED file has genotypes saved, there is no need for a VCF file as input.

* When PED file has genotypes saved, there is no need for a VCF file as input.

* '''famRvTest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html|'''Merlin'''] format. Please refer to [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.

* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html|'''Merlin'''] format. Please refer to [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.

* An example PED file is in the following:

* An example PED file is in the following:

     1 1 0 0 1 1.5 1 23 A A A A A A A A A A

     1 1 0 0 1 1.5 1 23 A A A A A A A A A A

===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 -p your.ped -d 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 -p your.ped -d 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 -p your.ped -d your.dat --SingleVarScore --SingleVarLRT --SingleVarWald --inverseNormal --useCovariates --traitName LDL --kinGeno

===Gene-level Association===

===Gene-level Association===

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 ==

== Change Log ==