Description Usage Arguments Value Author(s) References See Also Examples
View source: R/getExpInterval.R
Identifies the interval/support of relative substitution frequencies (RSFs) dominated by the second model component, i.e. by the probability of being induced by the experimental procedure. In addition, this function can be used to generate diagnostic plots of the model fit, representing (i) model densities and log odds ratio (ii) the posterior class probability, i.e. the probability of a given observation being generated by experimental induction.
1  getExpInterval(model, bayes = TRUE, leftProb, rightProb, plot = TRUE)

model 
A list containing the model as returned by the function

bayes 
Logical, if TRUE the Bayes classifier (cutoff at posterior class probabilities >= 0.5) is applied. If FALSE, custom cutoff values should be provided through leftProb and rightProb. Default is TRUE. 
leftProb 
Numeric, the posterior probability corresponding to the left boundary (start) of the high confidence RSF interval. 
rightProb 
Numeric, the posterior probability corresponding to the right boundary (end) of the high confidence RSF interval. 
plot 
Logical, if TRUE diagnostics plot showing the model components, log odds and the computed posterior with highlighted identified RSF interval are returned. 
A list with two numeric slots, corresponding to the extremes of the RSF interval (RSF support).
supportStart 
start of the high confidence RSF interval 
supportEnd 
end of the high confidence RSF interval 
Federico Comoglio and Cem Sievers
Sievers C, Schlumpf T, Sawarkar R, Comoglio F and Paro R. (2012) Mixture models and wavelet transforms reveal high confidence RNAprotein interaction sites in MOV10 PARCLIP data, Nucleic Acids Res. 40(20):e160. doi: 10.1093/nar/gks697
Comoglio F, Sievers C and Paro R (2015) Sensitive and highly resolved identification of RNAprotein interaction sites in PARCLIP data, BMC Bioinformatics 16, 32.
fitMixtureModel
getHighConfSub
estimateFDR
1 2 3 4 5 6 7 8 9 10  data( model )
#default
support < getExpInterval( model = model, bayes = TRUE, plot = TRUE )
support
#custom interval (based, e.g. on visual inspection of posterior class probability
# or evaluation of FDR using the estimateFDRF function)
support < getExpInterval( model = model, leftProb = 0.2, rightProb = 0.7, plot = TRUE )
support

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.