getPvals: Non-parametric estimation of the null distribution of G'

In bmansfeld/QTLseqR: QTL mapping using Bulk Segregant Analysis of Next Generation Sequencing data.

Description

The function is used by runGprimeAnalysis 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(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

bmansfeld/QTLseqR documentation built on Jan. 25, 2020, 8:52 p.m.