metapro

Introduction

The meta-analysis is conducted to increase the statistical power by combining evidences (e.g., effect sizes and p-values) obtained from multiple experiments. The p-value combination has been widely used for meta-analysis when effect sizes are not available. metapro is a CRAN R package that provides functions for p-value combinations. There are four functions including

wFisher : weighted Fisher's method
wZ : weighted Z-method
lancaster : Lancaster's procedure

The original Fisher's method and (weighted) Z-method have been commonly used for p-value combination. In particular, the Z-method is effective when a feature is associated with most of the cohorts. However, this attributes is disadvantageous detecting partially associated patterns (e.g., detection of African-specific features in trans-ethnic analysis).Therefore, in this study, we designed the ordmeta and wFisher method that work effectively in those situations. The detailed formulas are described in our paper.

Installation

Prerequisites

JAVA : If not installed yet, please install it first. Download: https://www.java.com/en/
Rtools (for Windows): Rtools are required for Windows users. Download: https://cran.r-project.org/bin/windows/Rtools/

After all prerequisites are installed, open R and install the metapro package by typing

install.packages('devtools') # install 'devtools'
library(devtools)
install_github('unistbig/metapro', INSTALL_opts=c("--no-multiarch"))
library(metapro) # Load metapro package

install.packages('metapro', INSTALL_opts=c("--no-multiarch")) 
library(metapro)

Tip: Dealing with Errors
In most cases, installation errors come from 1) encoding problem and 2) JAVA environment variable settings.
So, please try followings.

Encoding error
On Windows,

System locale setting modification: Click Start -> Control panel-> Clock and Region -> Region -> Administrative -> Change system locale... -> set 'Current system locale' as English (United States) and check the box in the below (Beta: Use Unicode UTF-8 for worldwide language support).
Reboot the PC, and execute Rstudio.
In the R console, type

Sys.setlocale('LC_ALL','C')

and install the package again.

Error from JAVA setting
Most error will occur with rJAVA. In this case, please

Check whether both JAVA and R are 64-bit, and
Set proper environment variable for JAVA_HOME, CLASSPATH, and RPATH.
Tip: System environment variable can be easily set by using Set.setenv() function in R. For example,

Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jdk1.8.0_211")
Sys.setenv(CLASSPATH="C:\\Program Files\\Java\\jdk1.8.0_211\\jre\\lib\\ext")
Sys.setenv(RPATH="C:\\Program Files\\R\\R-3.6.0\\bin\\x64")

If you are Linux or Mac OSX user, type following on terminal and re-open the R console after setting the environment variables.

sudo R CMD javareconf

Next, check whether rJAVA is installed correctly, and try installing metapro again.

install.packages('rJava')
library(rJava)

Usage

1. wFisher

wFisher is designed to assign weights to each experiment based on the sample size.

Example

wFisher(p=c(0.01, 0.02, 0.8, 0.25), weight = c(200, 500, 100, 80), is.onetail=FALSE, eff.sign = c(1,1,1,-1))
will return

$p
[1] 0.003060523

$overall.eff.direction
[1] "+"

Input Arguments and Values

Arguments
p	A numeric vector of p-values
is.onetail	Logical. If set TRUE, p-values are combined without considering the direction of effect, and vice versa. Default: TRUE.
weight	A numeric vector of weight or sample size for each experiment. Note! If no weight option is given, the original Fisher method is performed.
eff.sign	A vector of signs of effects. It works when is.onetail = FALSE

Value
p	Combined p-value
overall.eff.direction	The direction of combined effects.

2. wZ

Weighted Z-method. This function has been modified from sumz function in metap package.

Example

wZ(p=c(0.01, 0.02, 0.8, 0.25), weight = c(200, 500, 100, 80), is.onetail=FALSE, eff.sign = c(1,1,1,-1))
will return

[1] 0.001798156

$overall.eff.direction
[1] "+"

$sumz
[1] 2.911558

Input Arguments and Values

Arguments
p	A numeric vector of p-values
is.onetail	Logical. If set TRUE, p-values are combined without considering the direction of effect, and vice versa. Default: TRUE.
weight	A numeric vector of weight or sample size for each experiment. Note! If no weight option is given, the Stouffer's method is performed.
eff.sign	A vector of signs of effects. It works when is.onetail = FALSE

Value
p	Combined p-value
overall.eff.direction	The direction of combined effects.
sumz	Transformed sum of z-values

3. lancaster

Lancaster's procedure - the generalized version Fisher's method

Example

lancaster(p=c(0.01, 0.02, 0.8, 0.25), weight = c(200, 500, 100, 80), is.onetail=FALSE, eff.sign = c(1,1,1,-1))
will return

$p
[1] 0.005694935

$overall.eff.direction
[1] "+"

Input Arguments and Values

Arguments
p	A numeric vector of p-values
is.onetail	Logical. If set TRUE, p-values are combined without considering the direction of effect, and vice versa. Default: TRUE.
weight	A numeric vector of weight or sample size for each experiment. Required!
eff.sign	A vector of signs of effects. It works when is.onetail = FALSE

Value
p	Combined p-value
overall.eff.direction	The direction of combined effects.

Contact

Sora Yoon: ysora90@gmail.com
Department of Biological Sciences, UNIST