plot sequence logos stack

Description

plot sequence logos stack

Usage

1

Arguments

pfms

a list of position frequency matrices, pfms must be a list of class pfm

...

other parameters can be passed to plotMotifLogo function

Value

none

Examples

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  pcm1<-matrix(c(0,50,0,50,
           100,0,0,0,
           0,100,0,0,
           0,0,100,0,
           0,0,0,100,
           50,50,0,0,
           0,0,50,50), nrow=4)
  pcm2<-matrix(c(50,50,0,0,
           0,100,0,0,
           0,50,50,0,
           0,0,0,100,
           50,50,0,0,
           0,0,50,50), nrow=4)
  rownames(pcm1)<-c("A","C","G","T")
  rownames(pcm2)<-c("A","C","G","T")
  pfms<-list(p1=new("pfm",mat=pcm2pfm(pcm1),name="m1"),
         p2=new("pfm",mat=pcm2pfm(pcm2),name="m2"))
  pfms<-DNAmotifAlignment(pfms)
  plotMotifLogoStack(pfms)

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