EQF.permu {QTLEMM}

EQF Permutation

Description

The EQF matrix cluster permutation process for QTL hotspot detection.

Usage

EQF.permu(
  LOD.QTLdetect.result,
  ptime = 1000,
  alpha = 0.05,
  Q = TRUE,
  console = TRUE
)

Arguments

LOD.QTLdetect.result

list. The data list of the output from LOD.QTLdetect().

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.

bin

The bin information matrix used in this analysis.

LOD.threshold

The LOD threshold used in this analysis.

cluster.number

The number of QTLs in each cluster group.

cluster.id

The serial number of traits in each cluster group.

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

LOD.QTLdetect EQF.plot

Examples

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

# run and result
result <- EQF.permu(LOD.QTLdetect.result, ptime = 50)
result$cluster.number