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Nucleotide specific misincorporation rate

tx_add_misincRateNucSpec.Rd

Calculates the misincorporation rate from a reference nucleotide to an specific misincorporated nucleotide. For example, when looking for positions in cytidines that were read as thymine in RNA after bisulphite treatment.

Usage

tx_add_misincRateNucSpec(DT, refNuc, misNuc, minNucReads = 20)

Arguments

DT

data.table. A table as output by the tx_makeDT_nucFreq() or tx_makeDT_covNucFreq() functions.

refNuc

Reference nucleotide See tx_add_refSeqDT()

misNuc

Misincorporated nucleotide

minNucReads

Minimum number of nucleotides read needed to calculate misincorporation rate

Value

data.table