homologyScore: Computes homology scores

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/public_methods.R

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

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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 [email protected]

See Also

predictPPI

Examples

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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)

Bioconductor-mirror/Path2PPI documentation built on May 31, 2017, 9:43 p.m.