k2n_calc: Calculate number of Estimated Unique Counts (EUC's)...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/k2n_calc.R

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

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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.

Author(s)

Lukasz Jan Kielpinski, Nikos Sidiropoulos

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

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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")

sidiropoulos/RNAprobR-old documentation built on May 29, 2019, 9:58 p.m.