readNimblegen {Ringo} | R Documentation

## Function to read in Nimblegen Intensity Text Files

### Description

Function to read in Nimblegen Intensity Text Files into an `RGList`. Calls some other functions for actual reading of data. This function is to be used with two-color NimbleGen array data. Use the function `read.xysfiles` of the `oligo` package for single-color data.

### Usage

    readNimblegen(hybesFile, spotTypesFile, path = getwd(),
     headerPattern="# software=NimbleScan",verbose = TRUE, ...)

### Arguments

`hybesFile` | Name of the file describing the arrays. In `limma` this file would be called targets file.
`spotTypesFile` | spot types also used by `limma`
`path` | Path to directoy that hold the files `hybesFile`, `spotTypesFile` and also the intensity files. Set this to `NULL` if you prefer the arguments `hybesFile`, `spotTypesFile` and the file-name entries of the hybes file to be treated as absolute or relative file paths themselves.
`headerPattern` | string; pattern used to identify explantory header lines in the supplied pair-format files
`verbose` | logical; progress output to STDOUT?
`...` | further arguments passed on the `readNgIntensitiesTxt`

### Value

Returns raw intensity values in form of an `RGList`.

### Author(s)

Joern Toedling

### See Also

`rglist`, `readTargets`

### Examples

      exDir <- system.file("exData",package="Ringo")
      exRG <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
      print(exRG)

[Package Ringo version 1.42.1 Index]