get_qtns: Select pseudo-QTNs.

In amkusmec/FarmCPUpp: Perform GWAS Using the FarmCPU Model

Description

Use p-values estimated by quick_lm to select pseudo-QTNs for use as covariates in subsequent single-marker regression tests. Pseudo-QTNs may be selected using a set number of bins and a set number of pseudo-QTNs or may be optimized based on a set of optional sizes.

Usage

get_qtns(Y, GM, P, method, bin.sizes, nqtn, CV = NULL, GDP = NULL,
  theLoop = NULL)

Arguments

Y	A data frame with two columns. The first column contains taxa names. The second column contains numeric phenotypic values.
GM	A data frame with three columns: marker IDs, chromosome, and base-pair positions.
P	A numeric vector of marker p-values.
method	A character string, one of c("static", "optimum").
bin.sizes	A vector of possible bin sizes in base-pairs.
nqtn	A vector of possible numbers of pseudo-QTNs to select.
CV	A numeric matrix of user-specified covariates.
GDP	A pointer to a big.matrix object containing marker scores.
theLoop	The current iteration of the overal FarmCPU process. Controls bin size selection for method = "static".

Value

A logical vector specifying which markers have been chosen as pseudo-QTNs.

Author(s)

Zhiwu Zhang

Aaron Kusmec

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