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 [email protected]

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)
``` |

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

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