twoEightNormalize {dStruct} | R Documentation |
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. The raw reactivities are divided by the normalization factor to get normalized reactivities. This is called as 2-8 % normalization and has been a common way to normalize data from RNA structurome profiling technologies such as SHAPE-Seq, Structure-Seq, etc. (see Low and Weeks, 2010, Sloma et al., 2015, and Choudhary et al., 2017).
twoEightNormalize(raw.estimates)
raw.estimates |
A vector of raw reactivities. |
A vector of normalized reactivities.
Krishna Choudhary
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.
twoEightNormalize(c(NA, rnorm(20, 0.5, 0.3), NA, -999))