a better seqLogo
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berrylogo.Rproj

README.md

berrylogo: a better sequence logo

Build Status codecov DOI

Description

A berrylogo is a sequence logo alternative developed by Charles C. Berry for "Selection of Target Sites for Mobile DNA Integration in the Human Genome" [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664696](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664696/)

Instead of “information content”, the y-axis is the log relative frequency with respect to the background frequency, generated here from the gc_content parameter.

Installation

# Install latest commit from Github:
devtools::install_github("leipzig/berrylogo")

Usage

library("berrylogo")
freqs<-matrix(data=c(0.25,0.65,0.87,0.92,0.16,0.16,0.04,0.98,0.98,1.00,0.02,0.10,0.10,0.80,0.98,0.91,0.07,0.07,
             0.11,0.05,0.04,0.00,0.26,0.17,0.00,0.01,0.00,0.00,0.29,0.17,0.01,0.03,0.00,0.00,0.32,0.32,
             0.53,0.26,0.07,0.02,0.53,0.18,0.96,0.01,0.00,0.00,0.65,0.01,0.89,0.17,0.01,0.09,0.59,0.12,
             0.11,0.04,0.02,0.06,0.05,0.49,0.00,0.00,0.02,0.00,0.04,0.72,0.00,0.00,0.01,0.00,0.02,0.49),
             byrow=TRUE,nrow=4,dimnames=list(c('A','C','G','T')))
p<-berrylogo(freqs,gc_content=.41)
print(p)

Output

berrylogo