metaAnalysis {MetaCyto} | R Documentation

## Performs meta-analysis

### Description

A function that performs meta-analysis

### Usage

    metaAnalysis(value, variableOfInterst, otherVariables, studyID, data, CILevel,
      main, ifScale = c(TRUE, FALSE), cex = 1)

### Arguments

`value` | A string to specify the column name of the dependent variable (y)
`variableOfInterst` | A string to specify the column name of the independent variable of interest (x1)
`otherVariables` | A string vector to specify the column names of independent variables included in the regression model other than the variableOfInterst.
`studyID` | A string to specify the column name of study ID.
`data` | A data frame containing the data
`CILevel` | A number between 0 to 1, used to specify the confidence interval to be plotted in the forest plot.
`main` | A string to specify the title of the forest plot
`ifScale` | A vector of two logic values, specifying if the dependent variable and the variableOfInterst should be scaled when calculating the effect size.
`cex` | A number specifying the amount by which plotting text and symbols should be scaled relative to the default in the forest plot.

### Value

Returns data frame describing the effect size of variableOfInterst on value in each individual studies, as well as the over all effect size.

### Examples

    library(dplyr)
    #collect all summary statistics
    fn=system.file("extdata","",package="MetaCyto")
    files=list.files(fn,pattern="cluster_stats_in_each_sample",recursive=TRUE,
                     full.names=TRUE)
    fcs_stats=collectData(files,longform=TRUE)
    # Collect sample information
    files=list.files(fn,pattern="sample_info",recursive=TRUE,full.names=TRUE)
    sample_info=collectData(files,longform=FALSE)
    # join the cluster summary statistics with sample information
    all_data=inner_join(fcs_stats,sample_info,by="fcs_files")

    # plot forrest plot to see if the proportion of CCR7+ CD8 T cell
    # is affected by age (while controlling for Gender)
    L="CD3+|CD4-|CD8+|CCR7+"
    dat=subset(all_data,all_data$parameter_name=="fraction"&
                all_data$label==L)
    MA=metaAnalysis(value="value",variableOfInterst="Subject Age",main=L,
                    otherVariables=c("Gender"),studyID="study_id",
                    data=dat,CILevel=0.95,ifScale=c(TRUE,FALSE))

[Package MetaCyto version 1.4.0 Index]