glmAnalysis {MetaCyto} | R Documentation

## Perform generalized linear model analysis to estimate effect size.

### Description

A function that performs generalized linear model analysis to estimate effect size.

### Usage

    glmAnalysis(value = "value", variableOfInterst = "Subject Age", parameter,
      otherVariables = c("Gender"), studyID = "study", label = "label", data,
      CILevel = 0.95, ifScale = c(TRUE, FALSE))

### 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)
`parameter` | A string to specify what summary statistics is the dependent variable.
`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.
`label` | A string to specify the name the column that contains the cluster label or name.
`data` | A data frame containing the data. Usually a long form data frame returned by collectData.
`CILevel` | A number between 0 to 1, used to specify the confidence levels. e.g. 0.95 represent 95 percent confidence interval.
`ifScale` | A vector of two logic values, specifying if the dependent variable and the variableOfInterst should be scaled when calculating the effect size.

### Details

The function use the model value ~ variableOfInterst + otherVariables + studyID to estimate the effect size. Use it as a screening tool. Use metaAnalysis function to analyze an effect size in more detail.

### Value

Returns data frame describing the overall effect size of variableOfInterst on value. May be slightly different from the value reported from the function metaAnalysis.

### 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")
    # See the fraction of what clusters are affected by
    # age (while controlling for Gender)
    GA=glmAnalysis(value="value",variableOfInterst="Subject Age",
                  parameter="fraction",
                  otherVariables=c("Gender"),studyID="study_id",label="label",
                  data=all_data,CILevel=0.95,ifScale=c(TRUE,FALSE))

[Package MetaCyto version 1.4.1 Index]