Combine two p-values

Description

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 χ^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.

Usage

p.combine(p1, p2, method = c("fisher", "max", "average", "prod", "negfisher"))

Arguments

Value

p-values

Author(s)

Moritz Gerstung

Examples

p1 <- runif(1000)
p2 <- runif(1000)
hist(p1)
p.avg = p.combine(p1,p2, method="average")
hist(p.avg)
p.fish = p.combine(p1,p2, method="fisher")
hist(p.fish)
p.max = p.combine(p1,p2, method="max")
hist(p.max)
pairs(data.frame(p1,p2,p.fish,p.max,p.avg))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(deepSNV)
Loading required package: parallel
Loading required package: Rhtslib
Rhtslib htslib version 1.1
Loading required package: IRanges
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: XVector
Loading required package: VGAM
Loading required package: splines
Loading required package: VariantAnnotation
Loading required package: Rsamtools

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate


Attaching package: 'deepSNV'

The following objects are masked from 'package:VGAM':

    dbetabinom, pbetabinom

The following object is masked from 'package:BiocGenerics':

    normalize

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/deepSNV/p.combine.Rd_%03d_medium.png", width=480, height=480)
> ### Name: p.combine
> ### Title: Combine two p-values
> ### Aliases: p.combine
> 
> ### ** Examples
> 
> p1 <- runif(1000)
> p2 <- runif(1000)
> hist(p1)
> p.avg = p.combine(p1,p2, method="average")
> hist(p.avg)
> p.fish = p.combine(p1,p2, method="fisher")
> hist(p.fish)
> p.max = p.combine(p1,p2, method="max")
> hist(p.max)
> pairs(data.frame(p1,p2,p.fish,p.max,p.avg))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>