Qhot.EQF {QTLEMM}

EQF Matrix Conversion

Description

Convert the QTL flanking marker data to EQF matrix. And the EQF matrix cluster permutation process can be further carried out to detect QTL hotspots.

Usage

Qhot.EQF(
  DataQTL,
  Datachr,
  bin.size = 0.5,
  permu = TRUE,
  ptime = 1000,
  alpha = 0.05,
  Q = TRUE,
  console = 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.

Datachr

vector. The length of each chromosome(in cM).

bin.size

numeric. The bin size(in cM) for QTL detection. If the distance of flanking marker of a QTL is lass than the bin size, it will be mark in the EQF matrix and will participate in the cluster grouping process.

permu

logical. When set to TRUE, the function will carry out the cluster grouping process and cluster group permutation.

ptime

integer. The permutation times.

alpha

numeric. The type 1 error rate of detecting the hotspot.

Q

logical. When set to TRUE, the function will additionally carry out the permutation of the Q method as the control group, which will be indicated as 'B' in the output.

console

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

Value

EQF.matrix

The matrix denotes the EQF value of each bin for every QTL in this database.

bin

The bin information matrix whose first column denotes the chromosome number and the second column denotes the number of bins on that chromosome.

bin.size

The bin size set in this analysis.

EQF.trait

The matrix denotes the EQF value of each bin for every trait of this database.

EQF.detect

The matrix denotes the EQF value of each bin for the trait that have the QTL detected in the set bin size.

EQF.nondetect

The matrix denotes the EQF value of each bin for the trait that have no QTL detected in the set bin size.

cluster.matrix

The new EQF matrix after the clustering process.

permu.matrix.cluster

The permutation result of the clustering method, which has been sorted by order.

permu.matrix.Q

The permutation result of the Q method, which has been sorted by order.

EQF.threshold

The EQF threshold is calculated from the permutation process.

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>

See Also

Qhot EQF.plot

Examples

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

#' # run and result
result <- Qhot.EQF(QTL.example, chr.example, bin.size = 2, permu = TRUE, 
ptime = 100, alpha = 0.05, Q = FALSE)