calculate.rnaseh.activity: Calculate the fitness of the DNA-only gap-region in...

In Santaris/affinity: Functions to do thermodynamics on oligonucleotides

Description

For an input character vector of oligonucleotide sequences, this function calculates/predicts a score between 0 and 100. The higher the score, the better the fit to RNase H.

Usage

calculate.rnaseh.activity(oligos.lna)

Arguments

oligos.lna

A character vector of oligonucleotide sequences in camel-case (uppercase: LNA, lowercase: DNA) in the 5 to 3 direction.

Details

The calculation is based on a robust linear model fit to single-point knock-down data against a single target.

Value

Returns a numeric vector of same length as oligos.lna, with each entry between 0 (worst fit) and 100 (best fit).

Author(s)

Peter Hagedorn

Examples

data(publictm)

## select oligos from Stanton et al., 2012
i <-  grep("Stanton",publictm$IDstudy)

## calculate RNase H fit
pred.active <- calculate.rnaseh.activity(publictm$Sequence[i])

Santaris/affinity documentation built on May 9, 2019, 12:43 p.m.