plotRegion-methods: Plot of the region

Description Usage Arguments Value Examples

Description

Plot of the beta values againts their position. Data is taken from probe analysis. Cpgs with a p-value smaller than 0.05 (without adjusting) are blue and points with a p-value greater than 0.05 are red.

Usage

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plotRegion(object, variable = modelVariables(object)[[1]], range = NULL,
  main = paste("Region plot of ", variable))

Arguments

object

AnalysisResults or AnalysisRegionResults

variable

Character with the variable name used to obtain the probe results. Note: model name should be used. Original variable name might not be valid.

range

GenomicRange whose cpgs will be shown (only for AnalysisResults objects)

main

Character with the plot title.

Value

A plot is generated on the current graphics device.

Examples

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if (require(minfiData) & require(GenomicRanges)){
set <- prepareMethylationSet(getBeta(MsetEx), pheno = data.frame(pData(MsetEx)))
range <- GenomicRanges::GRanges(seqnames=Rle("chrY"), 
ranges = IRanges(3000000, end=12300000))
rangeNoSNPs <- DARegionAnalysis(set, variable_names = "sex", range = range)
plotRegion(rangeNoSNPs)
}

MEAL documentation built on May 31, 2017, 11:16 a.m.