getNgsColorsInfo: Helper function to extract color information for filenames on...

Description Usage Arguments Details Value Author(s)

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

1
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 <[email protected]>


benilton/oligo-release documentation built on May 12, 2019, 10:59 a.m.