p.combine

One of "fisher" (default), "max" or "average"

method


This function combines two P-values into a single one using a statistic defined by method.
"fisher" uses the product of the two, in this case the logarithm of the product is
$\chi^2_4$ distributed. If the method = "max", the resulting P-value is $\max\{P_1,P_2\}^2$.
For method = "average" the mean is used, yielding a P-value of $2 x^2$ if $x=(P_1+P_2)/2 < .5$
and  $1-2 x^2$ otherwise. "negfisher" is the negative of Fisher's method using $1-F(1-P_1, 1-P_2)$, where $F$ is the combination
function of Fisher's method; for small $P_1,P_2$, the result is very similar to method="average". Fisher's method behaves a bit like a logical AND
of the joint null-hypothesis, whereas negative Fisher is like an OR.


This package provides provides quantitative variant callers for
detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing
experiments. The deepSNV algorithm is used for a comparative setup with a
control experiment of the same loci and uses a beta-binomial model and a
likelihood ratio test to discriminate sequencing errors and subclonal SNVs.
The shearwater algorithm computes a Bayes classifier based on a
beta-binomial model for variant calling with multiple samples for
precisely estimating model parameters such as local error rates and
dispersion and prior knowledge, e.g. from variation data bases such as
COSMIC.

Moritz Gerstung

deepSNV

Detection of subclonal SNVs in deep sequencing data.

p.combine function

This function combines two P-values into a single one using a statistic defined by method.
"fisher" uses the product of the two, in this case the logarithm of the product is
$\chi^2_4$ distributed. If the method = "max", the resulting P-value is $\max{P_1,P_2}^2$.
For method = "average" the mean is used, yielding a P-value of $2 x^2$ if $x=(P_1+P_2)/2 < .5$
and  $1-2 x^2$ otherwise. "negfisher" is the negative of Fisher's method using $1-F(1-P_1, 1-P_2)$, where $F$ is the combination
function of Fisher's method; for small $P_1,P_2$, the result is very similar to method="average". Fisher's method behaves a bit like a logical AND
of the joint null-hypothesis, whereas negative Fisher is like an OR.

p.combine: Combine two p-values

Description

Usage

Arguments

Value

Examples