SMA: Performs Single Marker Association tests for both Linear...

In marf-at-vt/GWAS.BAYES: Bayesian analysis of Gaussian GWAS data

Performs Single Marker Association tests for both Linear Mixed Models and Linear models.

Description

Performs Single Marker Association tests for both Linear Mixed Models and Linear models.

Usage

SMA(Y, SNPs, kinship = FALSE, P3D = FALSE)

Arguments

Y	The observed numeric phenotypes
SNPs	The SNP matrix, where each column represents a single SNP encoded as the numeric coding 0, 1, 2. This is entered as a matrix object.
kinship	The observed kinship matrix, has to be a square positive semidefinite matrix. Defaulted as the identity matrix. The function used to create the kinship matrix used in the BICOSS paper is A.mat() from package rrBLUP.
P3D	Population previous determined, if TRUE BICOSS uses approximated variance parameters estimated from the baseline model when conducting both the screening and the model selection steps. Setting P3D = TRUE is significantly faster. If FALSE, uses exact estimates of the variance parameters all models in both the screening and model selection step.

Value

The p-values corresponding to every column provided in SNPs. These p-values can be used with any threshold of your choosing or with p.adjust().

marf-at-vt/GWAS.BAYES documentation built on Jan. 31, 2023, 4:04 p.m.