homologyScore {Path2PPI} | R Documentation

## 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

`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.

### 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)

[Package Path2PPI version 1.12.0 Index]