Hi, I am new to R and looking for some help in plotting multiple bed files which may or may not overlap. They do have multiple chromosomes. I found a package called Gviz, where a Chromosome ideogram and genomic region could be plotted. But I am not sure how to load a bed file.
I am aiming to plot plain bed files(chr ,start,stop) to see which regions are overlapping in multiple bed files I have.
From below example code I see they loaded two data sets called cpgislands and genemodel (believe that comes with package), like wise is there a way to load my bed files to plot them?
data(**cpgIslands**) atr <- AnnotationTrack(**cpgIslands**, name="CpG") gtr <- GenomeAxisTrack() itr <- IdeogramTrack(genome="mm9", chromosome="chr1") data(**geneModels**) grtr <- GeneRegionTrack(**geneModels**, name="Gene Model", showId=TRUE) plotTracks(list(itr, gtr, atr, grtr))
Please help me with this. Thanks.