LRTthre {QTLEMM}

LRT Threshold

Description

The LRT threshold for QTL interval mapping based on the Gaussian stochastic process (Kao and Ho 2012).

Usage

LRTthre(
  marker,
  type = "RI",
  ng = 2,
  cM = TRUE,
  ns = 200,
  gv = 25,
  speed = 1,
  simu = 1000,
  d.eff = FALSE,
  alpha = 0.05,
  console = TRUE
)

Arguments

marker

matrix. A k*2 matrix contains the marker information, where the row dimension 'k' represents the number of markers in the chromosomes. The first column labels the chromosomes where the markers are located, and the second column labels the positions of markers (in morgan (M) or centimorgan (cM)). It's important to note that chromosomes and positions must be sorted in order.

type

character. The population type of the dataset. Includes backcross (type="BC"), advanced intercross population (type="AI"), and recombinant inbred population (type="RI"). The default value is "RI".

ng

integer. The generation number of the population type. For instance, in a BC1 population where type="BC", ng=1; in an AI F3 population where type="AI", ng=3.

cM

logical. Specify the unit of marker position. If cM=TRUE, it denotes centimorgan; if cM=FALSE, it denotes morgan.

ns

integer. The number of individuals for generating the individual trait values. Changes in this value do not significantly affect the outcome of the LRT threshold value.

gv

numeric. The genetic variance for generating the individual trait values. Changes in this value do not significantly affect the outcome of the LRT threshold value.

speed

numeric. The walking speed of the QTL analysis (in cM).

simu

integer. Determines the number of simulation samples that will be used to compute the LRT threshold using the Gaussian process.

d.eff

logical. Specifies whether the dominant effect will be considered in the parameter estimation for AI or RI population.

alpha

numeric. The type I error rate for the LRT threshold.

console

logical. Determines whether the process of the algorithm will be displayed in the R console or not.

Value

The LRT threshold for QTL interval mapping.

References

KAO, C.-H. and H.-A. Ho 2012 A score-statistic approach for determining threshold values in QTL mapping. Frontiers in Bioscience. E4, 2670-2682. <doi: 10.2741/e582>

See Also

rmvnorm

Examples

# load the example data
load(system.file("extdata", "exampledata.RDATA", package = "QTLEMM"))

# run and result
LRTthre(marker, type = "RI", ng = 2, speed = 2, simu = 60)