gtWAS:Genome and Transcriptome Wide Association Study
Quantitative trait loci mapping and genome wide association analysis are used to find candidate molecular
marker or region associated with phenotype based on linkage
analysis and linkage disequilibrium. Gene expression
quantitative trait loci mapping is used to find candidate
molecular marker or region associated with gene expression. In
this package, we applied the method in Liu W. (2011)
<doi:10.1007/s00122-011-1631-7> and Gusev A. (2016)
<doi:10.1038/ng.3506> to genome and transcriptome wide
association study, which is aimed at revealing the association
relationship between phenotype and molecular markers,
expression levels, molecular markers nested within different
related expression effect and expression effect nested within
different related molecular marker effect. F test based on full
and reduced model are performed to obtain p value or likelihood
ratio statistic. The best linear model can be obtained by
stepwise regression analysis.
