plotEWAS-methods: Plot a Manhattan plot with the probe results

Description Usage Arguments Value Examples

Description

Plot log p-value for each chromosome positions. Highlighting cpgs inside a range is allowed.

Usage

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plotEWAS(object, variable = modelVariables(object)[[1]], range = NULL,
  main = paste("Manhattan 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 highlighted

main

Character with the plot title.

Value

A plot is generated on the current graphics device.

Examples

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if (require(minfiData)){
betas <- getBeta(MsetEx)[floor(seq(1, nrow(MsetEx), 10000)), ]
set <- prepareMethylationSet(betas, pheno = data.frame(pData(MsetEx)))
methyOneVar <- DAPipeline(set, variable_names = "sex", probe_method = "ls")
plotEWAS(methyOneVar)
}

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

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