Design_file_parser: Design file parser

In cghRA: Array CGH Data Analysis and Visualization

Description

These functions are examples of design file parsers, as can be used directly or by tk.design to produce a cghRA.probes object from a CGH design file.

Usage

  Agilent.design(file, name = NULL, organism = as.character(NA),
    assembly = as.character(NA), chromosomes = NULL, ...)
  custom.design(file, name = NULL, organism = as.character(NA),
    assembly = as.character(NA), chromosomes = NULL, ...)

Arguments

file	Single character value, path to the file to extract the design from (Agilent TDT design file for Agilent.design, CSV file as described below for custom.design).
name	Single character value, the name of the design. NULL will generate an automatic design name with the array dimensions (e.g. "Agilent 125 x 50").
organism	Single character value, the name of the organism studied by the current design.
assembly	Single character value, the genome assembly version for probe coordinates.
chromosomes	Character vector, the ordered list of the chromosome names for the design organism. If NULL the factor levels of the chrom column will be extracted, if not chromosomes will be used as levels to coerce the chrom column to factor.
...	Further arguments are ignored by Agilent.design and custom.design, but can be used by other design file parsers.

Details

As the package was developed with Agilent arrays, only the corresponding parser and a generic one are currently provided. Parsing design files from other brands can be achieved providing a custom design file parser suiting the manufacturer file format. Common brand file parsers may be added in the future, if you developed one (or need one to be developed) and wish it to be added to the package, please contact the package maintainer.

"Custom" files must be CSV files, using tabulations as column separators, periods as decimal separators and a first row naming columns. No comment line is allowed, and cell content protection (quoting) can be performed using double-quotes. The mandatory columns are "chrom" (character), "start" (integer) and "end" (integer), describing the genomic location of each probe in the design. Additionally it is recommended to provide "strand" ("+", "-" or NA), "id" (an integer ID that will be used to match probes between design and data files), "name" (character), "row" and "col" (integers, the physical position of the probe on the slide). Further columns will be stored as provided.

Value

An object of class cghRA.design.

Author(s)

Sylvain Mareschal

See Also

cghRA.design-class, tk.design

cghRA documentation built on May 2, 2019, 3:34 a.m.