Make a Volcano plot with the probe results

Description

Plot log p-value versus the change in expression/methylation.

Usage

1
2
plotVolcano(object, variable = modelVariables(object)[1], mindiff = NULL,
  main = paste("Volcano plot of", variable, "results"))

Arguments

object

MethylationResults or MethylationRegionResults

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.

mindiff

Numeric with the minimum change in methylation or expression needed to be significant

main

Character with the plot title.

Value

A plot is generated on the current graphics device.

Examples

1
2
3
4
5
6
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")
plotVolcano(methyOneVar)
}

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.