maxEnt-class: Class '"maxEnt"'

In wokai/spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

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")

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.