The function is used by runGprimeAnalysis_local to
estimate p-values for the weighted G' statistic based on the
non-parametric estimation method described in Magwene et al. 2011.
Breifly, using the natural log of Gprime a median absolute deviation (MAD)
is calculated. The Gprime set is trimmed to exclude outlier regions
(i.e. QTL) based on Hampel's rule. An alternate method for filtering out
QTL is proposed using absolute delta SNP indeces greater than a set
threshold to filter out potential QTL. An estimation of the mode of the
trimmed set is calculated using the mlv function
from the package modeest. Finally, the mean and variance of the set are
estimated using the median and mode and p-values are estimated from a
log normal distribution.
Usage
getPvals_local(
Gprime,
deltaSNP = NULL,
outlierFilter = c("deltaSNP", "Hampel"),
filterThreshold
)Arguments
- Gprime
a vector of G prime values (tricube weighted G statistics)
- deltaSNP
a vector of delta SNP values for use for QTL region filtering
- outlierFilter
one of either "deltaSNP" or "Hampel". Method for filtering outlier (ie QTL) regions for p-value estimation
- filterThreshold
The absolute delta SNP index to use to filter out putative QTL