get_qtns: Select pseudo-QTNs.

Description Usage Arguments Value Author(s)

View source: R/get_qtns.R

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

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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.