mppR: mpp_perm – R documentation

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mpp_perm

QTL significance threshold by permutation

Description

Determination of an empirical null distribution of the QTL significance threshold for a MPP QTL analysis using permutation test (Churchill and Doerge, 1994).

Usage

mpp_perm(mppData, trait = 1, Q.eff = "cr", N = 1000, q.val = 0.95,
  verbose = TRUE, n.cores = 1)

Arguments

`mppData`	An object of class `mppData`.
`trait`	`Numerical` or `character` indicator to specify which trait of the `mppData` object should be used. Default = 1.
`Q.eff`	`Character` expression indicating the assumption concerning the QTL effects: 1) "cr" for cross-specific; 2) "par" for parental; 3) "anc" for ancestral; 4) "biall" for a bi-allelic. For more details see `mpp_SIM`. Default = "cr".
`N`	Number of permutations. Default = 1000.
`q.val`	Single `numeric` value or vector of desired quantiles from the null distribution. Default = 0.95.
`verbose`	`Logical` value indicating if progression of the function should be printed. It will not affect the printing of the other functions called by `mpp_perm()`, especially the printing of `asreml()`. Default = TRUE.
`n.cores`	`Numeric`. Specify here the number of cores you like to use. Default = 1.

Details

Performs N permutations of the trait data and computes each time a genome-wide QTL profile. For every run, it stores the highest -log10(p-val). These values can be used to build a null distribution for the QTL significance threshold. Quantile values can be determined from the previous distribution. For more details about the different possible models and their assumptions see mpp_SIM documentation.

Value

Return:

List with the following object:

`max.pval`	Vector of the highest genome-wide -log10(p-values).
`q.val`	Quantile values from the QTL significance threshold null distribution.
`seed`	`Numeric` vector of random generated seed values for each permutation.

Author(s)

Vincent Garin

References

Churchill, G. A., & Doerge, R. W. (1994). Empirical threshold values for quantitative trait mapping. Genetics, 138(3), 963-971.

Examples

data(mppData)

Perm <- mpp_perm(mppData = mppData, Q.eff = "cr", N = 5)

mppR

Multi-Parent Population QTL Analysis

v1.2.1

GPL-3

Authors

Vincent Garin [aut, cre], Valentin Wimmer [aut], Dietrich Borchardt [ctb, dtc], Fred van Eeuwijk [ctb, ths], Marcos Malosetti [ctb, ths]

Initial release

2020-02-10