GEP.process: MLPA peak detection

In MLPA: Multiplex Ligation-Dependent Probe Amplification Data Analysis

Description

GEP.process handles the whole analysis from .fsa files, generating tables of expression values and graphical profiles.

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

Usage

  GEP.process(input, design, output, overwrite = list(), gene.cex = 1.3,
    file.line = 3, mar = c(5,4,5,1), progressBar = NULL)
  GEP.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.
overwrite	Named list, to be passed to designFile().
gene.cex	Single numeric value, the character expanding factor for gene names.
file.line	Single numeric value, the line on which print the file name on plots.
mar	Numeric vector with 4 values, the margin sizes on bottom, left, top and right sides respectively.
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.

Value

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

Various files are produced, in location set by the output argument :

~.expr.tsv

Numeric matrix of normalized expressions (each sample is divided by its means).

~.peaks.tsv

Table collecting all the peaks called during the analysis, with their size, intensity, sample, annotation and off-scale status.

~.pdf

Profiles of the samples analysed. See designFile for customisation.

~.log

Log file of errors, warnings and message (only GEP.interface produces it).

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

  # Working in temporary directory
  output <- sprintf("%s/test.log", tempdir())
  
  # See files before analysis
  dir(system.file("extdata", package="MLPA"))
  
  # Launch analysis in package directory
  GEP.process(
    input = system.file("extdata/fsa", package="MLPA"),
    design = system.file("extdata/design.conf", package="MLPA"),
    output = output
  )
  
  # List resulting files
  dir(dirname(output), full.names=TRUE)

MLPA documentation built on May 2, 2020, 1:06 a.m.