prior: Set marker p-values based on prior expectations.
In amkusmec/FarmCPUpp: Perform GWAS Using the FarmCPU Model

prior

R Documentation

Set marker p-values based on prior expectations.

Description

Modifies marker p-values calculated by the GLM based on prior expectations.

Usage

prior(GM, P = NULL, Prior = NULL)

Arguments

`GM`	A dataframe with three columns containing the SNP ID, chromosome, and base-pair position of each marker.
`P`	A numeric vector containing marker p-values.
`Prior`	A dataframe with four columns. The first three correspond to the columns of `GM` and the fourth contains prior probabilities.

Details

If Prior is NULL, p-values are not modified. Marker p-values are multiplied by the user-provided prior p-values. A value of 1 will not modify the p-values calculated by the GLM.