49 lines
1.6 KiB
R
49 lines
1.6 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/wrapper.R
|
|
\name{div_lambda_GC}
|
|
\alias{div_lambda_GC}
|
|
\title{Return lambda_GC for different numbers of PCs for GWAS on Panicum virgatum.}
|
|
\usage{
|
|
div_lambda_GC(
|
|
df,
|
|
type = c("linear", "logistic"),
|
|
snp,
|
|
svd = NA,
|
|
ncores = 1,
|
|
npcs = c(0:10),
|
|
saveoutput = FALSE
|
|
)
|
|
}
|
|
\arguments{
|
|
\item{df}{Dataframe of phenotypes where the first column is sample.ID and each
|
|
sample.ID occurs only once in the dataframe.}
|
|
|
|
\item{type}{Character string. Type of univarate regression to run for GWAS.
|
|
Options are "linear" or "logistic".}
|
|
|
|
\item{snp}{A bigSNP object with sample.IDs that match the df.}
|
|
|
|
\item{svd}{big_SVD object; Covariance matrix to include in the regression.
|
|
Generate these using \code{bigsnpr::snp_autoSVD()}.}
|
|
|
|
\item{ncores}{Number of cores to use. Default is one.}
|
|
|
|
\item{npcs}{Integer vector of principle components to use.
|
|
Defaults to c(0:10).}
|
|
|
|
\item{saveoutput}{Logical. Should output be saved as a csv to the
|
|
working directory?}
|
|
}
|
|
\value{
|
|
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.
|
|
}
|
|
\description{
|
|
Given a dataframe of phenotypes associated with sample.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.
|
|
}
|