Description Usage Arguments Details Value See Also Examples
View source: R/discovery.log.R
A set of functions with different assumptions on the probability of RNA in situ staining, given a sequencing coverage.
1 2 3  discovery.log(seq, saturate = 60, bias = 0.01)
discovery.linear(seq, saturate = 60, bias = 0.01)
discovery.identic(seq, saturate=Inf, bias=0)

seq 
A vector of sequencing FPKMs. 
saturate 
FPKM value from which on maximum discovery probability (=0.99) is assumed (i.e. almost certain true positives). Value of 60 is default, may need adjustment to sequencing coverage. 
bias 
Positive staining probability of 0 FPKM transcripts (i.e. false positives). Must be >0. Default is 0.01, an empirically determined value. 
discovery.log Uses a logarithmic saturation function for discovery probabilities. This relationship was empirically determined from sequencing and hybridisation data.
discovery.linear Linear saturation function for discovery probabilities.
discovery.identic Passes input through. Useful for comparing RNASeq Vs. RNASeq data. Also for cases when the discovery probability for each transcript has been already determined in some other way.
A vector of probabilities. Element names are preserved.
1 2 3 4 5 6 7  plot(0:80, discovery.log(0:80),
ylim=c(0,1.1), type="l",
xlab="FPKM", ylab="p(discovery insitu hybridization)")
plot(0:80, discovery.linear(0:80),
ylim=c(0,1.1), type="l",
xlab="FPKM", ylab="p(discovery insitu hybridization)")

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