nim.read {aCGH.Spline} | R Documentation |
Function to read a Nimblgen "SEG_MNT.txt" file.
nim.read(file, Raw)
file |
- Nimblegen "SEG_MNT.txt" file to read. |
Raw |
- to use raw data or not (TRUE or FALSE). |
This function reads the contains of a Nimblegen "SEG_MNT.txt" file into a ".temp" formatted dataframe and flags low intensity probes.
The ".temp" dataframe contains eight columns:
- Log2 ratio values.
- Cy5 intensity values.
- Cy3 intensity values.
- Chromosome number.
- Start position.
- Stop position.
- An index.
- A flag.
This function reads spatially normalised intensity values from the Nimblegen input file.
There is currently no option to output a "SEG_MNT.txt" format, however, signal-map gff format is supported.
Tomas William Fitzgerald
# data <- nim.read("Nimblegen_SEG_MNT.txt")