README.md

In fchuffar/methmybeachup: Easily convolves methylome signal

methmybeachup

The methmybeachup package provides a set of functions allowing to easily convolves and vizualise methylome signal across genes and CpG islands

Data

Data set is extracted from GSE51954 Vandiver AR, Irizarry RA, Hansen KD, Garza LA et al. Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biol 2015 Apr 16;16:80. PMID: 25886480

Installation

To get the current development version from github, you need first to install devtools. Then, install methmybeachup:

install.packages("devtools")
devtools::install_github("fchuffar/methmybeachup")

Example

layout(1)
library(methmybeachup)

cols = as.numeric(sunexp_design$sex) * 2
names(cols) = rownames(sunexp_design)
gene = genes[6,]
res1 = analyse_meth(gene, sunexp_data, sunexp_platform, cols, PLOT=TRUE)
legend("topright", col=as.numeric(unique(sunexp_design$sex)) * 2, legend=unique(sunexp_design$sex), lty=1)

layout(matrix(1:9, 3), respect=TRUE)
foo = apply(genes, 1, analyse_meth, sunexp_data, sunexp_platform, cols, PLOT=TRUE)

fchuffar/methmybeachup documentation built on May 16, 2019, 12:07 p.m.