35 lines
1.2 KiB
R
35 lines
1.2 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/wrapper.R
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\name{div_gwas}
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\alias{div_gwas}
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\title{Wrapper for bigsnpr for GWAS}
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\usage{
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div_gwas(df, snp, type, svd, npcs)
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}
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\arguments{
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\item{df}{Dataframe of phenotypes where the first column is sample.ID}
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\item{snp}{Genomic information to include for wheat.}
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\item{type}{Character string. Type of univarate regression to run for GWAS.
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Options are "linear" or "logistic".}
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\item{svd}{Optional covariance matrix to include in the regression. You
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can generate these using \code{bigsnpr::snp_autoSVD()}.}
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\item{npcs}{Integer. Number of PCs to use for population structure correction.}
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}
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\value{
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The gwas results for the last phenotype in the dataframe. That
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phenotype, as well as the remaining phenotypes, are saved as RDS objects
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in the working directory.
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}
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\description{
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Given a dataframe of phenotypes associated with sample.IDs, this
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function is a wrapper around bigsnpr functions to conduct linear or
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logistic regression on wheat. The main advantages of this
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function over just using the bigsnpr functions is that it automatically
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removes individual genotypes with missing phenotypic data
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and that it can run GWAS on multiple phenotypes sequentially.
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}
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