biGaussianNull: biGaussianNull

Description Usage Arguments Value

View source: R/bayeslabel.R

Description

Compute a prior null distribution without given any prior biological knowledge. Methods used to estimate this prior include: "biGaussian","biGaussianWith0Cutoff","biGaussianMean0","biGaussianModeSplit" etc.

Usage

1
2
biGaussianNull(rstat, null.quantile = c(0.25, 0.75),
  method = c("biGaussianMean0", "biGaussianModeSplit"))

Arguments

rstat

The observed test statistics.

null.quantile

Data quantiles, pre-fixed so that we could reduce the impact of extreme values for estimating prior null distribution. Default value is c(0.25, 0.75).

method

A char. The methods we used to do estimation: either "biGaussian"– EM algorithm for mixtures of two univariate normals, or "biGaussianWith0Cutoff"– assume all negative test statistics forms one normal and all positive test statistics forms the other one normal. And proportion parameter is proportional to a number of observations each class, or "biGaussianMean0"– null is formed by two half normals. "biGaussianModeSplit"– split data from median value, then flip each part to the other side to estimate normal distribution.

Value

A list with element

alpha

cutoff value (if given)

mu

mean positon for two normals

sd

sd value for two normals

prop

proportion for each normal


BANFF documentation built on May 29, 2017, 11:59 a.m.

Related to biGaussianNull in BANFF...