getNgsColorsInfo: Helper function to extract color information for filenames on...
In jmacdon/oligo: Preprocessing tools for oligonucleotide arrays
Description
Usage
Arguments
Details
Value
Author(s)
View source: R/utils-general.R
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 <bcarvalh@jhsph.edu>
jmacdon/oligo documentation built on Aug. 11, 2020, 12:32 a.m.
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Description Usage Arguments Details Value Author(s)
View source: R/utils-general.R
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 |
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>
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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