vignettes/coMET-package.R

In TiphaineCMartin/coMET_original: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

\name{coMET-package}
\alias{coMET-package}
\alias{coMET}
\docType{package}
\title{
an R plotting package to visualize regional plots of epigenome-wide association scan results
}
\description{
  The coMET is a R package to visualize the EWAS (epigenome-wide association scans) results in a genomic region. coMET package generates the plots of association, co-methylation patterns and a series of annotation tracks at genomic scale.

}
\details{
\tabular{ll}{
Package: \tab comet\cr
Type: \tab Package\cr
Version: \tab 0.99.0\cr
Date: \tab 2014-10-03\cr
License: \tab GPL (>=2)\cr
Url: \tab http://comet.epigen.kcl.ac.uk:3838/coMET/ \cr
}
coMET package that can generate the regional plot capturing the features
of co-methylation patterns, EWAS results, and genomic information.A
coMET figure includes plot of p-value from the EWAS result, provides
customized annotation tracks, and a triangle heatmap plot which
demonstrates the correlation structure of CpG sites in a genomic region,
calculated by the pairwise Spearman’s rank correlation method.Plots are
created as PDF,EPS files.

A list containing two items: config.var and gbl.var, which includes the values of all significant variables used by coMET.
}
\author{
Tiphaine Martin, Idil Yet, Pei-Chien Tsai, Jordana T. Bell

Maintainer: Tiphaine Martin <tiphaine.martin@kcl.ac.uk>
Website: http://www.epigen.kcl.ac.uk/comet
}

\references{
Martin, T.C, Erte, I, Tsai, P-C, Bell, J.T.,coMET: an R plotting package to visualize regional plots of epigenome-wide association scan results, QC14, 2014.
}
~~ Optionally other standard keywords, one per line, from file KEYWORDS in the R documentation directory ~~
\keyword{ package }
\seealso{
~~ Optional links to other man pages, e.g. ~~
~~ \code{\link[<coMET>:<coMET>-package]{<coMET>}} ~~
}
\examples{
library(Gviz)
configfile <- "../inst/extdata/config_cyp1b1_zoom_4comet.txt" 
chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg19"

genetrack <-genesENSEMBL(gen,chrom,start,end,showId=FALSE)
snptrack <- snpBiomart(chrom, start, end, 
                       dataset="hsapiens_snp_som",showId=FALSE)
strutrack <- structureBiomart(chrom, start, end, 
                              strand, dataset="hsapiens_structvar_som")
clinVariant<-ClinVarMainTrack(gen,chrom,start,end)
clinCNV<-ClinVarCnvTrack(gen,chrom,start,end)
gwastrack <-GWASTrack(gen,chrom,start,end)
geneRtrack <-GeneReviewsTrack(gen,chrom,start,end)

listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
                 clinCNV,gwastrack,geneRtrack)
comet(config.file=configfile,TRACKS.GVIZ=listgviz, 
      VERBOSE=FALSE, PRINT.IMAGE=FALSE,DISP.PVALUEPLOT=FALSE)
}