ftr2xys: Convert a NimbleScan ftr-file into a xys-file

In Ringo: R Investigation of ChIP-chip Oligoarrays

Description

Auxiliary function to convert a NimbleScan feature-report file into a xys-file that can be used with the function read.xysfiles of package oligo.

Usage

ftr2xys(ftr.file, path=getwd())

Arguments

ftr.file	character; file path of feature report file to convert into an xys file
path	file path to directory where the xys-file should be written to; defaults to the current working directory

Details

The output file is names as the input ftr file; with the file extension .ftr replaced by .xys.

Value

Function returns only NULL invisibly and is only called for its side effect to write the xys-file into the current working directory.

Note

This function should only be used with one-color Nimblegen microarrays and when the correct xys-file of the raw data is not available. The output file can be used with the function read.xysfiles of package oligo.

Author(s)

Joern Toedling

Examples

 ## Not run: 
   sapply(list.files(pattern=".ftr$"),ftr2xys)
   library(oligo)
   fs = read.xysfiles(list.xysfiles())
 
## End(Not run)

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.