PATOWAS include four function calculation modules: 1) kinship matrix calculation(km_calc), 2) variance component analysis(vc_anal), 3) omics wide p-value scanning for main additive effect(ps_main), and 4) omics wide p-value scanning for interaction effect(ps_inter).
PATOWAS was dedicatedly developed to analyze phenotypic trait through omics wide association stuides, which need one of data matrix file such as 1) additive genotypic data, 2) gene expression data , or 3) metabolite abundance data as the inputs to calculate the 2 kinship matrices: ka, kaa, and furthermore need the trait related phenotypic data file to estimate the variance component ratios and p-value scanning for main additive and interaction effects.
All of the function modules are developed in C++ in a cross-open source IDE Code:: Blocks and have been successfully compiled and tested in our linux system. User can freely download, modify and compile the source code without restriction into their own pipeline.
Six original datasets(Two phenotypes Yield and KGW across three associative omics) were submitted to PATOWAS; and another two reduced expression (1543 genes) with two phenotypic data are also submitted to PATOWAS. Each result include two kinship matrix (Ka and Kaa), variance component analysis result, 1D and 2D p-value scanning results.
The genotype data and the phenotype trait data can be analyzed by other GWAS tools, TASSEL based GWAS results for YIELD and KGW are also provided, which are very consistent to the 1D G2P results by PATOWAS