dmr_genome_plot: dmr_genome_plot
In ND91/ndlib: A list of handy functions

Description Usage Arguments Value Author(s) See Also Examples

View source: R/dmr_genome_plot.R

Produces a dotplot of a specific (region of) CpG(s) given a matrix of beta-values superposed onto the RefSeq genomic location.

dmr_genome_plot(
  name,
  chr,
  betas,
  annotation.gr,
  factor_interest,
  start_dmr,
  end_dmr,
  flanks,
  SNP = F,
  dmps = F,
  genome_version = "hg19",
  biomart = NULL,
  diff_symbol = T,
  dotsize = 0.7,
  plotgrid = T,
  confint = T,
  highlight = T,
  col_DMR = NULL
)

`name`	Name of the DMR/DMP
`chr`	Chromosome (example "chr6")
`betas`	Matrix of Beta with the CpG numbers as rownames
`annotation.gr`	GenomicRanges object containing the annotation/features of the GMset (obtained through minfi::getAnnotation())
`factor_interest`	A vector based on which you want to stratify your plot
`start_dmr`	The start of the region you want to plot
`end_dmr`	The end of the region you want to plot. If the region is only 1 bp, simply enter the same value as the start_dmr
`flanks`	How large should the flanking region be? Defaults to the same size as the DMR.
`SNP`	Do you want SNP information sourced from UCSC? Defaults to FALSE, because calling UCSC is slow.
`dmps`	Do you want to indicate them individually? Defaults to FALSE
`genome_version`	Which genome build to use? Defaults to "hg19"
`biomart`	A biomart object. If NULL (default), the gene coordinates will be obtained from RefSeq.
`diff_symbol`	Do you want the different groups to be represented by different symbols (TRUE)? Defaults to FALSE
`dotsize`	The pixel size for plotting symbols. Defaults to 0.7 (standard of Gviz)
`plotgrid`	Do you want to plot a grid (TRUE)? Defaults to TRUE
`confint`	Do you want to plot the 95% confidence intervals (TRUE)? Defaults to TRUE
`highlight`	Do you want to highlight the region of interest (TRUE)? Defaults to TRUE
`col_DMR`	A color vector used for plotting the DMRs. Must be the same size as the levels of factor_interest. Defaults to NULL (which is automatic color assignment)

A dotplot of a specific (region of) CpG(s) of beta-values superposed onto the RefSeq genome. Additionally, it returns a genomic ranges object with the CpGs within the chosen region.

Andrew Y.F. Li Yim

minfi

minfiData

#Load data
require(minfiData)
baseDir <- system.file("extdata", package = "minfiData")
targets <- read.metharray.sheet(base = baseDir)
RGset <- read.metharray.exp(targets = targets, recursive = T)
Mset <- preprocessIllumina(rgSet = RGset, bg.correct = T, normalize = "controls", reference = 2)
Rset <- ratioConvert(Mset)
GMset <- mapToGenome(Rset)

Beta <- getBeta(GMset)
annotation.gr <- makeGRangesFromDataFrame(getAnnotation(GMset), keep.extra.columns = T, start.field = "pos", end.field = "pos")

#Find DMRs
design <- model.matrix(~pData(Mset)$Sample_Group)
bumps <- bumphunter(object = GMset, design = design, coef = 2, cutoff = 0.2, B = 0, type = "Beta")
dmr <- bumps$table[1,]

#Plot DMP
dmr_genomeplot(name = "DMR_1", chr = "chr6", betas = Beta, factor_interest = pData(Mset)$Sample_Group, annotation.gr = annotation.gr, start_dmr = dmr$start, end_dmr = dmr$start)

#Plot DMR (without SNPs)
dmr_genomeplot(name = "DMR_1", chr = "chr6", betas = Beta, factor_interest = pData(Mset)$Sample_Group, annotation.gr = annotation.gr, start_dmr = dmr$start, end_dmr = dmr$end)

#Plot DMR (with SNPs)
dmr_genome_plot(name = "DMR_1", chr = "chr6", betas = Beta, factor_interest = pData(Mset)$Sample_Group, annotation.gr = annotation.gr, start_dmr = dmr$start, end_dmr = dmr$end, SNP = T)