summary.scanonebins: Estimate FDR LOD thresholds from a 'scanonebins' object.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

This function is based on the R/qtl function mqmscanfdr (see reference below), but uses a precalculated scanonebins object instead of running permutations directly.

Usage

## S3 method for class 'scanonebins'
summary(object, scanone.result, lodcolumns = NULL,
  fdr = 0.01, ...)

Arguments

object	A scanonebins object.
scanone.result	A scanone object created from the same data that was used to create the scanonebins object.
lodcolumns	In a scanone or equivalent object, this parameter indicates which LOD columns to consider. In other objects with LOD-column-associated elements, this parameter indicates which of those LOD-column-associated elements to consider. The specified LOD columns must be a character vector of LOD column names, a logical vector with length equal to the number of LOD columns, or a numeric vector of indices with respect to the set of LOD columns. If no LOD columns are specified, all are used.
fdr	False discovery rates for which an approximate LOD thresholds should be estimated.
...	Unused arguments.

Details

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).

Value

A summary.scanonebins matrix containing LOD thresholds that correspond approximately to the specified false discovery rates.

References

Arends D, Prins P, Jansen RC, Broman KW (2010) R/qtl: high-throughput multiple QTL mapping. Bioinformatics 26(23):2990-2. (PubMed)

gact/shmootl documentation built on Nov. 11, 2021, 6:23 p.m.