MEAL (version 1.2.3)

plotEWAS: Plot a Manhattan plot with the probe results

Description

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

Usage

plotEWAS(object, variable = modelVariables(object)[[1]], range = NULL)

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

Value

A plot is generated on the current graphics device.

Examples

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