maxEnt-class {spliceSites} | R Documentation

## Class `"maxEnt"`

### Description

Provides methods for calculation of Splice-site scores. Both functions (`score5` and `score3`) are intended to work on the '+' strand. `score5` scores the 5' side (i.e. the splice donor, left) and the `score3` scores the 3' side (i.e. the splice acceptor, right).

### Creation of `maxEnt` objects

Objects can be created by `load.maxEnt()`.

### Slots

`ev`:

  Object of class `"environment"` Contains external score data.

`basedir`:

  Object of class `"character"` Directory from which external data is restored.

### Methods

basedir

  `signature(x = "maxEnt")`: Returns basedir value.

basedir<-

  `signature(x = "maxEnt",value="character")`: Sets basedir value.

score5

  `signature(x = "maxEnt",seq="character",pos="integer")`: Calculates score5 value for seq at given position.

scoreSeq5

  `signature(x="maxEnt",seq="character",frame="integer")`: Calculates score5 values for a single sequence and a series of positions (frame).

score3

  `signature(x = "maxEnt",seq="character",pos="integer",which="character")`: Calculates score3 value for seq at given position. Accepted values for which are: "ent","wmm" and "emm".

scoreSeq3

  `signature(x = "maxEnt",seq="character",frame="integer",which="character")`: Calculates score3 values for a single sequence and a series of positions (frame). Accepted values for which are: "ent","wmm" and "emm".

### Author(s)

Wolfgang Kaisers

### Examples

    mes<-load.maxEnt()
    score5(mes,"CCGGGTAAGAA",4)                  # 9.844127
    score3(mes,"CTCTACTACTATCTATCTAGATC",pos=20) # 6.706947

    # scoreSeq functions
    sq5<-scoreSeq5(mes,seq="ACGGTAAGTCAGGTAAGT")
    sq3<-scoreSeq3(mes,seq="TTTATTTTTCTCACTTTTAGAGACTTCATTCTTTCTCAAATAGGTT")

[Package spliceSites version 1.31.0 Index]