getNgsColorsInfo: Helper function to extract color information for filenames on...
In oligo: Preprocessing tools for oligonucleotide arrays

Description Usage Arguments Details Value Author(s)

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.

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

`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`

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.

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.

Benilton Carvalho <bcarvalh@jhsph.edu>

oligo documentation built on Nov. 8, 2020, 6:52 p.m.