Module Description

• 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.

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Test Dataset

• Omics Markers for Genotype Data RIL_Genotypes , Gene Expression Data RIL_Expressions , Metabolite Abundance Profiling Data RIL_Metabolites
• Phenotypic Data for 1) Yield, 2) KGW, 3) Grain, 4) Tiller
• Mapping of expressed genes to genotype bins Gene_GenotypeBin_Map
• Reduced Gene Expression Data (One gene in one genotype bin) for 1) Reduced_RIL_Expression_Yield, 2) Reduced_RIL_Expression_KGW

PATOWAS Results

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.

• PATOWAS Result for Genotype_YIELD (Size 6.4MB)
• PATOWAS Result for Genotype_KGW (Size 6.4MB)
• PATOWAS Result for Expression_YIELD (Size 1.3GB, Warning!!! Large Size)
• PATOWAS Result for Expression_KGW (Size 1.2GB, Warning!!! Large Size)
• PATOWAS Result for Metabolite_YIELD (Size 2.7MB)
• PATOWAS Result for Metabolite_KGW (Size 2.7MB)
• PATOWAS Result for Reduced_Expression_YIELD (Size 7.5MB)
• PATOWAS Result for Reduced_Expression_KGW (Size 7.5MB)

TASSEL Results for G2P

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

• TASSEL Result for TASSEL_G2P_YIELD TASSEL_G2P_KGW

Source Code

• All of the source code have been archived into a package and can be downloaded from PATOWAS_Source_Code

Matlab Scripts for 1D and 2D Genetic Effect Illustration

• Scripts and example data to illustrate 1D Association Plot of Main Effect and 2D Association Plot of Interaction Effect