RNAprobR (version 1.4.0)

k2n_calc: Calculate number of Estimated Unique Counts (EUC's) corresponding to given number of observed unique barcodes.

Description

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.

Usage

k2n_calc(merged_file, unique_barcode_file, output_file)

Arguments

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)

Value

If output_file specified function writes a file, if not - returns a vector.

References

Kielpinski, L.J., and Vinther, J. (2014). Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res.

See Also

readsamples

Examples

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")