substitute_pvalue: Substitute p-values for pseudo-QTNs.

In amkusmec/FarmCPUpp: Perform GWAS Using the FarmCPU Model

Substitute p-values for pseudo-QTNs.

Description

Replace the p-values calculated for pseudo-QTNs according to one of several rules.

Usage

substitute_pvalue(GM, GLM, QTN = NULL, method = "mean", npc = 0)

Arguments

GM	A dataframe with three columns containing the SNP ID, chromosome, and base-pair position of each marker.
GLM	A FarmCPUpp object returned by quick_lm.
QTN	A three column matrix containing the SNP ID, chromosome, and base-pair position of each pseudo-QTN.
method	A character scalar, one of "penalty", "reward", "mean", "median", or "onsite".
npc	An integer scalar. The number of user-defined covariates.

Details

Fill in details.

Value

The input GLM object with the pseudo-QTN p-values in GLM[["P"]] substituted.

Author(s)

Xiaolei Liu

Zhiwu Zhang

Aaron Kusmec

amkusmec/FarmCPUpp documentation built on Dec. 16, 2024, 9:01 a.m.