Qhot {QTLEMM}

QTL Hotspot

Description

This function generates both numerical and graphical summaries of the QTL hotspot detection in the genomes, including information about the flanking markers of QTLs.

Usage

Qhot(DataQTL, DataCrop, ScanStep = 1, NH = 100, NP = 1000, save.pdf = TRUE)

Arguments

DataQTL

data.frame. A data frame with 5 columns for QTL information. The columns represent the serial number of QTLs, the trait names, the chromosome numbers, the left flanking marker positions(in cM) of QTLs, and the right flanking marker positions(in cM) of QTLs.

DataCrop

data.frame. A data frame with 3 columns for chromosome information consists of the chromosome names, the center positions(in cM) and the lengths of chromosomes.

ScanStep

numeric. A value for the length(cM) of every bin.

NH

integer. A value for the number of spurious hotspots in the proposed method.

NP

integer. A value for permutation times to calculate the threshold.

save.pdf

logical. When set to TRUE, the PDF file of plots will be saved in the working directory instead of being displayed in the console.

Value

EQF

The expected QTL frequency(EQF) in every bin per chromosome.

P.threshold

The EQF thresholds for proposed method.

Q.threshold

The EQF thresholds for the Q method.

nHot

The numbers of detected hotspots per chromosome for the proposed method and Q method.

Graphical outputs for visualizing the summarized results includes the expected QTL frequency of scan steps, and the composition of QTLs for different traits in the detected hotspots.

Note

This program may generate a large amount of graphical output. To manage this, it's recommended to save the results in a PDF file using the "save.pdf" argument.

References

Wu, P.-Y., M.-.H. Yang, and C.-H. KAO 2021 A Statistical Framework for QTL Hotspot Detection. G3: Genes, Genomes, Genetics: jkab056. <doi: 10.1093/g3journal/jkab056>

Examples

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

# run and result
result <- Qhot(QTL.example, crop.example, 5, 20, 100, save.pdf = FALSE)