2.3 GWAS

It’s required to provide genotype, map (if applicable), and phenotype files to run GWAS in iPat. Covariates and kinship matrix are optional. User-provided covariates will serve as fixed effects in the GWAS model. Often time users are not recommended to provide a kinship matrix, since those implemented tools will generate one automatically and user-define kinship is used only in ‘MLM’ and ‘CMLM’ from GAPIT.

Output files from GWAS include:

2.3.1 GAPIT

## Column 1 ['V1'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for  backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
## Column 1 ['V1'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for  backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
TABLE 2.1: Arguments for GAPIT
Arguments Default Options Description
Model GLM GLM, MLM, CMLM, FarmCPU Implemented models: general linear model (GLM), mixed linear model (MLM), compressed mixed linear model (CMLM), and FarmCPU.
PC 3 Ranges between 3 to 10 Principal components to control spurious signals caused by population stratifications

Fig. Configuration for GAPIT

Reference

  • Tang,Y. et al. (2016) GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction. Plant J., 9.

2.3.2 FarmCPU

## Column 1 ['V1'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for  backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
## Column 1 ['V1'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for  backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
TABLE 2.2: Arguments for FarmCPU
Arguments Default Options Description
Method bin optimum static, optimum
maxLoop 10 Ranges between 1 to 10 Number of iterations for FarmCPU to detect QTNs

Fig. Configuration for FarmCPU

Reference

  • Liu,X. et al. (2016) Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies. PLoS Genet., 12 , e1005767