| Qhot {QTLEMM} | R Documentation |
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)