find.mean.up: Helper function for getParams

In leekgroup/derfinder: Differential expression analysis of RNA-seq data at base-pair resolution

Description

Finds mean of the distribution of statistics generated from overexpressed nucleotides

Usage

find.mean.up(init.value, null.mean, null.sd, null.prop, vals)

Arguments

init.value	number in (0.5, 1) representing a percentile of the null distribution to use as starting value
null.mean	estimated mean of null distribution (usually found with locfdrFit)
null.sd	estimated standard deviation of null distribution (usually found with locfdrFit)
null.prop	estimated proportion of statistics that came from the null distribution
vals	vector of all the observed values from the mixture distribution

Details

This function is for experienced users or debugging only - all other users should use getParams, which calls this function.

Value

If numerical method succeeds, a list with elements

If numerical method fails, a list with elements

m	estimated mean of the underexpressed distribution, and
p	the percentile of the null distribution used to find this mean

If numerical method fails, a list with elements

m	mean of underexpressed distribution, as estimated by the 5th percentile of the estimated null distribution
s	standard deviation of underexpressed distribution, as estimated by the standard deviation of the null distribution

Author(s)

Alyssa Frazee

See Also

getParams, find.mean.down, find.sd

leekgroup/derfinder documentation built on May 20, 2019, 11:30 p.m.