mpp_perm {mppR} | R Documentation |
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 |
trait |
|
Q.eff |
|
N |
Number of permutations. Default = 1000. |
q.val |
Single |
verbose |
|
n.cores |
|
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 |
|
Author(s)
Vincent Garin
References
Churchill, G. A., & Doerge, R. W. (1994). Empirical threshold values for quantitative trait mapping. Genetics, 138(3), 963-971.
See Also
Examples
data(mppData)
Perm <- mpp_perm(mppData = mppData, Q.eff = "cr", N = 5)