getNgsColorsInfo: 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
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.
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.