remove_qtns: Remove highly correlated pseudo-QTNs.

In amkusmec/FarmCPUpp: Perform GWAS Using the FarmCPU Model

Description

Removes highly correlated pseudo-QTNs based on the Pearson correlation coefficients between marker scores. In each pair of highly correlated markers, the marker with the lower p-value is retained.

Usage

remove_qtns(GDP = NULL, GM = NULL, seqQTN = NULL, seqQTN.p = NULL,
  threshold = 0.99)

Arguments

GDP	A pointer to a big.matrix object containing the marker scores.
GM	A data frame with three columns: marker ID, chromosome, and base-pair position.
seqQTN	An integer vector of columns in GDP that have been selected as pseudo-QTNs.
seqQTN.p	A numeric vector of p-values for the pseudo-QTNs.
threshold	A numeric scalar. Pairs of pseudo-QTNs with correlation coefficients above this value will be pruned.

Value

An integer vector specifying the columns in GDP that are selected as pseudo-QTNs.

Author(s)

Zhiwu Zhang

Aaron Kusmec

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