PhenStatReport {PhenStat} | R Documentation

## Generating a pdf report from a PhenList object

### Description

This function takes a Phenlist object and generates a pdf report containing several statistical methods.

### Usage

      PhenStatReport(
        PhenlistObject           ,
        depVariable = NULL       ,
        other.response = NULL    ,
        update = TRUE            ,
        Gene.Symbol = NULL       ,
        Response.name = NULL     ,
        destination = NULL       ,
        reportTitle = "Extended Statistical Report",
        DataRelease = NULL       ,
        Showsource = FALSE       ,
        open = FALSE             ,
        clean = TRUE             ,
        verbos = FALSE           ,
        ...
      )

### Arguments

`PhenlistObject` | A phenlist object that is already created by PhenList() function in PhenStat.
`depVariable` | String. Name of the dependent variable.
`other.response` | The vector of strings. A vector of names containing the other dependent variables in the data set. Default NULL
`update` | Logical flag. Set to TRUE to get the latest version of the report on the fly. Default is TRUE
`Gene.Symbol` | Optional string. Gene symbol. Default NULL
`Response.name` | Optional string. Name of the dependent variable. Default NULL
`destination` | Location of the final report file. The default is the working directory of R.
`reportTitle` | The title of the report that is printed on the top of the first page of the report.
`DataRelease` | Optional flag. Data release version. Default NULL
`Showsource` | Logical flag. Set to TRUE to see the actual R codes that generate each section of the report. Default FALSE
`open` | Logical flag. Set to TRUE to open the report after it is generated. Default FALSE
`clean` | Logical flag. Set to TRUE to remove the auxiliary files after successfully generating the report. Default TRUE
`verbos` | Logical flag. Setting to TRUE shows the details and progress of the report generating function on screen. Default FALSE
`...` | List of other parameters that can be passed to the functions.

### Details

See PhenStatReport page on the IMPC website

### Value

`PhenlistObject` | The input object
`depVariable` | Dependent variable
`texfile` | The location of the .tex file, given Clean=FALSE
`pdffile` | The location of the final pdf file
`...` | The same as the input parameters

### Author(s)

Hamed Haselimashhadi <hamedhm@ebi.ac.uk>

### See Also

`PhenList`

### Examples

        file <- system.file("extdata", "test1.csv", package = "PhenStat")
        test = PhenStat:::PhenList(dataset = read.csv(file,na.strings = '-'),
                                   testGenotype = "Sparc/Sparc")
     ## Not run:
        PhenStatReport(test,
                       depVariable = 'Bone.Area',
                       open = TRUE)

    ## End(Not run)

[Package PhenStat version 2.17.0 Index]