k2n_calc {RNAprobR} | R Documentation |
Function calculates EUC's for each number of observed barcodes accounting for differential ligation probability of different barcodes. Function k2n_calc() writes file with a vector in which an i-th element is an estimated unique count given observing i unique barcodes.
k2n_calc(merged_file, unique_barcode_file, output_file)
merged_file |
path to merged_temp file containing 4 column: 1) RNAid, 2) Start, 3) End, 4) Barcode sequence (required) |
unique_barcode_file |
character with path to unique_barcode file (required) |
output_file |
name of a file to be generated (if specified [recommended] function will write a file, if not - function will return a vector) |
If output_file specified function writes a file, if not - returns a vector.
Lukasz Jan Kielpinski, Nikos Sidiropoulos
Kielpinski, L.J., and Vinther, J. (2014). Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res.
write(c("DummyRNA\t1\t1\tA", "DummyRNA\t1\t1\tC", "DummyRNA\t2\t2\tG", "DummyRNA\t2\t2\tT"),file="dummy_merged_file") write(c("DummyRNA\t1\t1\t2", "DummyRNA\t2\t2\t2"), file="dummy_unique_barcode") k2n_calc(merged_file = "dummy_merged_file", unique_barcode_file = "dummy_unique_barcode")