Description Usage Arguments Details Value References
This function is based on the R/qtl function mqmscanfdr
(see
reference below), but uses a precalculated scanonebins
object
instead of running permutations directly.
1 2 3 |
object |
A |
scanone.result |
A |
lodcolumns |
In a |
fdr |
False discovery rates for which an approximate LOD thresholds should be estimated. |
... |
Unused arguments. |
Thresholds are set from the bin edges of the scanonebins
object, and
empirical false-discovery rates (FDRs) are calculated at these thresholds.
For each false-discovery rate specified in the fdr
parameter, the
threshold with the next lowest FDR estimate is returned where possible, or
next highest FDR estimate otherwise. Summary results take NA
values
in cases where no sensible FDR can be returned (e.g. fewer loci above a
threshold in the main scanone result than in the corresponding permutation
results).
A summary.scanonebins
matrix containing LOD thresholds that
correspond approximately to the specified false discovery rates.
Arends D, Prins P, Jansen RC, Broman KW (2010) R/qtl: high-throughput multiple QTL mapping. Bioinformatics 26(23):2990-2. (PubMed)
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