PhenStatReport: Generating a pdf report from a PhenList object

In PhenStat: Statistical analysis of phenotypic data

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 <[e-mail]>

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)

PhenStat documentation built on Nov. 8, 2020, 8:13 p.m.