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kcha/seqLogo.R

Last active August 29, 2015 14:07
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seqLogo.R
#install if necessary
source("http://bioconductor.org/biocLite.R")
biocLite("seqLogo")
biocLite("Biostrings")
library(seqLogo)
library(Biostrings)
strings <- c("GATTACA", "GATAACA", "GATAAAA", "GATTAGA")
set <- DNAStringSet(strings)
pfm <- consensusMatrix(set)[DNA_BASES,]
seqLogo(pfm / colSums(pfm))
seqLogo(pfm / colSums(pfm), ic.scale = FALSE)
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