Computes homology scores

Description

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.

Usage

homologyScore(e.value, h.range)

Arguments

Details

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))

Value

Numeric vector containing the scores.

Author(s)

Oliver Philipp MolBI-software@bioinformatik.uni-frankfurt.de

See Also

predictPPI

Examples

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(Path2PPI)
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Path2PPI/homologyScore.Rd_%03d_medium.png", width=480, height=480)
> ### Name: homologyScore
> ### Title: Computes homology scores
> ### Aliases: homologyScore
> 
> ### ** Examples
> 
> 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)
[1] 0.00 0.25 0.50 0.75 1.00
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>