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LPEadj (version 1.32.0)

A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.

Description

Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment.

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Version

Version

1.32.0

License

LGPL

Maintainer

Carl Murie

Last Published

February 15th, 2017

Functions in LPEadj (1.32.0)

adjBaseOlig.error.step2

Evaluates LPE variance function of M for quantiles of A within and experimental condition. It is based on the adaptive number of intervals.
calculateLpeAdj

Evaluates local pooled error significance test with user chosen variance adjustments.
adjBaseOlig.error

Evaluates LPE variance function of M for quantiles of A within and experimental condition and then interpolates it for all genes.
lpeAdj

High level lpeAdj function that executes the adjusted local pooled error significance test. If more control over parameters is needed then see documentation for calculateLpeAdj.
adjBaseOlig.error.step1

Evaluates LPE variance function of M for quantiles of A within and experimental condition by dividing the A in 100 intervals.