normalizer {dStruct}R Documentation

Returns normalizer for reactivity vector.

Description

Assesses normalization factor for raw reactivities using the 2-8 % method. Given a reactivity profile, first, remove 2% of the nucleotides with the highest reactivities. Then, the normalization factor is the mean of reactivities of the 8% of the nucleotides with the next highest reactivities.

Usage

normalizer(raw.estimates)

Arguments

raw.estimates

A vector of raw reactivities.

Value

The normalization factor.

Author(s)

Krishna Choudhary

References

Low JT, Weeks KM. SHAPE-directed RNA secondary structure prediction. Methods. 2010; 52(2):150–8.

Sloma MF, Mathews DH, Chen SJ, Burke-Aguero DH. Chapter four – improving RNA secondary structure prediction with structure mapping data. In: Methods in Enzymology, vol. 553. Cambridge: Academic Press: 2015. p. 91–114.

Choudhary K, Deng F, Aviran S. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. Quant Biol. 2017; 5(1):3–24.

Examples

normalizer(c(NA, rnorm(20, 0.5, 0.3), NA, -999))

[Package dStruct version 0.99.3 Index]