generic.process: Processing multiple FSA files

In FSAtools: Fragment Analysis and Capillary Sequencing Tool Kit

Processing multiple FSA files

Description

generic.process handles the whole analysis of a series of .fsa files according to the pipeline described in the user-provided design file, generating tabular and graphical profiles.

generic.interface summons a Tcl-Tk interface to call generic.process interactively.

Usage

  generic.process(input, design, output, include = NULL, exclude = NULL,
     progressBar = NULL)
  generic.interface()

Arguments

input	Single character value, the path to a directory containing .fsa files to analyse. Notice it will be explored recursively, so sub-directories are allowed.
design	Single character value, the path to a design file, as handled by designFile.
output	Single character value, the path to a ".pdf" or ".log" file that will be created during the analysis.
include	Single character value, a regular expression files (with relative path) in input must match to be processed (ignored if NULL).
exclude	Single character value, a regular expression files (with relative path) in input must not match to be processed (ignored if NULL).
progressBar	A ttkprogressbar to increment during the processing, or NULL. This argument is only provided to connect GEP.interface and GEP.process, thus it should be ignored.

Details

The content of the analysis pipeline is fully controlled by the design file, see designFile for details and the examples section below for two working examples provided in the package.

More generally, generic.process loops over the list of .fsa files in the input directory and calls the requested functions one after the other, updating the fsa object at each step.

Value

Return nothing. generic.process raise errors, warnings and messages which are intercepted by generic.interface and redirected to the log file (output.log).

Author(s)

Sylvain Mareschal

References

Mareschal, Ruminy et al (2015) <doi:10.1016/j.jmoldx.2015.01.007> "Accurate Classification of Germinal Center B-Cell-Like/Activated B-Cell-Like Diffuse Large B-Cell Lymphoma Using a Simple and Rapid Reverse Transcriptase-Multiplex Ligation-Dependent Probe Amplification Assay: A CALYM Study"

See Also

designFile

Examples

  ### EXAMPLE 1 : Gene expression (RT-MLPA) ###
  
  # Working in temporary directory
  output <- sprintf("%s/GEP", tempdir())
  
  # See files before analysis
  dir(system.file("extdata", package="FSAtools"))
  
  # Launch analysis in package directory
  generic.process(
    input = system.file("extdata/fsa_GEP", package="FSAtools"),
    design = system.file("extdata/design_GEP.conf", package="FSAtools"),
    output = output
  )
  
  # List resulting files
  dir(dirname(output), full.names=TRUE)
  
  
  ### EXAMPLE 2 : Genotyping ###
  
  # Working in temporary directory
  output <- sprintf("%s/SNP", tempdir())
  
  # See files before analysis
  dir(system.file("extdata", package="FSAtools"))
  
  # Launch analysis in package directory
  generic.process(
    input = system.file("extdata/fsa_SNP", package="FSAtools"),
    design = system.file("extdata/design_SNP.conf", package="FSAtools"),
    output = output
  )
  
  # List resulting files
  dir(dirname(output), full.names=TRUE)

FSAtools documentation built on Aug. 19, 2023, 1:06 a.m.