bim.fdr {bim}R Documentation

Bayesian False Discovery Rate for QTL mapping

Description

Bayesian false discover rate (FDR) applied to QTL mapping. Use plot.bim.fdr to determine FDR for HPD level used in plot.bim.effects.

Usage

bim.fdr(x, cross, nqtl = 1, pattern = NULL, exact = FALSE, chr,
  ..., levels=<<see below>>,df=3,  qtl = <<see below>>)
plot.bim.fdr(x, cross, ..., fdr = <<see below>>,
  critical.value=<<see below>>, hpd = NULL )

Arguments

x object of class bim
cross corresponding object of class cross
nqtl subset on number of QTL
pattern subset on chromosome pattern of QTL
exact subset on exact pattern or number of QTL if true
chr subset of chromosomes to plot (numerical indices or chromosome names)
levels probability levels for HPD regions (default every 1 percent)
df degrees of freedom for smoothing spline estimator of prior on size
qtl QTL estimate information from bim.qtl
fdr object returned by call to bim.fdr
critical.value pFDR guidelines (ignored if hpd provided; default every .05 to .25)
hpd HPD guidelines
... graphical parameters can be given as arguments to plot

Details

FDR follows ideas of Storey (http://www.stat.berkeley.edu/~storey) adapted to Bayesian setting.

Value

bim.fdr returns an enhanced version of the bim.qtl object, with additional elements:

levels HPD levels
size relative size of HPD region across levels
fdr false discover rate across levels
hyp estiamtes for probabilities of hypotheses H0: no QTL at locus, M0: no QTL anywhere, M1: QTL somewhere
prob cumulative prior probability
spline spline estimate of cumulative prior probability
hyp estiamtes for probabilities of hypotheses H0: no QTL at locus, M0: no QTL anywhere, M1: QTL somewhere
fdr FDR for corresponding HPD levels (chosen by hpd or critical[value settings)

Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

References

http://www.stat.wisc.edu/~yandell/qtl/software/Bmapqtl

See Also

plot.bim.effects,bim.qtl

Examples

data( vern )
data( verngeo.bim )

plot.bim.fdr( verngeo.bim, vern, pattern=c(1,1) )

[Package bim version 1.01-1 Index]