maxEnt-class {spliceSites} | R Documentation |
"maxEnt"
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).
maxEnt
objectsObjects can be created by load.maxEnt()
.
ev
:Object of class "environment"
Contains external score data.
basedir
:Object of class "character"
Directory from which external data is restored.
signature(x = "maxEnt")
: Returns basedir value.
signature(x = "maxEnt",value="character")
: Sets basedir value.
signature(x = "maxEnt",seq="character",pos="integer")
: Calculates score5 value for seq at given position.
signature(x="maxEnt",seq="character",frame="integer")
: Calculates score5 values for a single sequence and a series of positions (frame).
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".
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".
Wolfgang Kaisers
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")