getNgsColorsInfo {oligo} | R Documentation

## Helper function to extract color information for filenames on NimbleGen arrays.

### Description

This function will (try to) extract the color information for NimbleGen arrays. This is useful when using `read.xysfiles2` to parse XYS files for Tiling applications.

### Usage

    getNgsColorsInfo(path = ".", pattern1 = "_532", pattern2 = "_635", ...)

### Arguments

`path` | path where to look for files
`pattern1` | pattern to match files supposed to go to the first channel
`pattern2` | pattern to match files supposed to go to the second channel
`...` | extra arguments for `list.xysfiles`

### Details

Many NimbleGen samples are identified following the pattern sampleID_532.XYS / sampleID_635.XYS.

The function suggests sample names if all the filenames follow the standard above.

### Value

A data.frame with, at least, two columns: 'channel1' and 'channel2'. A third column, 'sampleNames', is returned if the filenames follow the sampleID_532.XYS / sampleID_635.XYS standard.

### Author(s)

Benilton Carvalho <bcarvalh@jhsph.edu>

[Package oligo version 1.54.1 Index]