Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/public_methods.R
Computes the homology scores based on the BLAST E-value. This function is used
by the predictPPI
method to compute homology scores to decide whether
an interaction in a reference species is adopted to the target species
(see package vignette for a detailed description). It can be used to test
which E-values lead to which scores given a predefined E-value range.
1 | homologyScore(e.value, h.range)
|
e.value |
One BLAST E-value or a numeric vector with different BLAST E-values |
h.range |
Numeric vector consisting of two values. The first value indicates the lower bound (smallest E-value). Each E-value which is equal or less than this bound is scored with 1. The second value indicates the upper bound (biggest E-value). Each E-value which is equal or greater than this bound is scored with 0. |
Uses a linear function to map the E-value v to the range [l,u] where l is the lower and u the upper bound:
s(v)=|m*log_10(v)+b|
m=1/(log_10(l)-log_10(u))
b=-(m*log_10(u))
Numeric vector containing the scores.
Oliver Philipp MolBI-software@bioinformatik.uni-frankfurt.de
1 2 3 4 5 6 | l <- 1e-100 #lower bound
u <- 1e-20 #upper bound
h.range <- c(l,u) #define range
e.values <- c(1e-20,1e-40,1e-60,1e-80,1e-100) #some BLAST E-values
homologyScore(e.values,h.range)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.