Description Usage Arguments Value
Given a dataframe of phenotypes associated with PLANT_IDs and output from a PCA to control for population structure, this function will return a .csv file of the lambda_GC values for the GWAS upon inclusion of different numbers of PCs. This allows the user to choose a number of PCs that returns a lambda_GC close to 1, and thus ensure that they have done adequate correction for population structure.
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df |
Dataframe of phenotypes where the first column is PLANT_ID and each PLANT_ID occurs only once in the dataframe. |
type |
Character string. Type of univarate regression to run for GWAS. Options are "linear" or "logistic". |
snp |
Genomic information to include for Panicum virgatum. SNP data is available at doi:10.18738/T8/ET9UAU |
covar |
Covariance matrix to include in the regression. You
can generate these using |
ncores |
Number of cores to use. Default is one. |
npcs |
Integer vector of principle components to use. Defaults to c(0:10). |
saveoutput |
Logical. Should output be saved as a csv to the working directory? |
A dataframe containing the lambda_GC values for each number of PCs specified. This is also saved as a .csv file in the working directory.
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