STTtoShapeParameter

numeric indicating soft truncation threshold (STT) to
    convert to gamma parameter (must be 


In using the Gamma Method[4], a soft truncation threshold (STT) must be
specified (that is, shape parameter for gamma distribution). For
combining p values using Fisher's method, set STT to 1/e. Based on
simulation studies, we have found that STT between 0.10 and 0.20 achieve
optimal power for a variety of situations. Empirical p values for the
gene set association are determined via permutations.<p></p><p>This function is called by the pcgamma one.</p>

GSAgm is an R package that completes a self-contained gene set analysis (GSA) for RNA-seq and SNP data using the Gamma Method.

Rama Raghavan

GSAgm

Gene Set Analysis using the Gamma Method

STTtoShapeParameter function

numeric indicating soft truncation threshold (STT) to
    convert to gamma parameter (must be <= 0.4)


In using the Gamma Method[4], a soft truncation threshold (STT) must be
specified (that is, shape parameter for gamma distribution). For
combining p values using Fisher's method, set STT to 1/e. Based on
simulation studies, we have found that STT between 0.10 and 0.20 achieve
optimal power for a variety of situations. Empirical p values for the
gene set association are determined via permutations.

This function is called by the pcgamma one.

STTtoShapeParameter: Soft Truncation Threshold

Description

Usage

Arguments

Examples