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

Description Usage Arguments Details Value Author(s)

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

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

`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.

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.

A numeric vector of updated marker p-values.

Zhiwu Zhang

Aaron Kusmec

amkusmec/FarmCPUpp documentation built on Dec. 25, 2021, 10:05 p.m.