plotMethylationProfileFromData {DMRcaller} | R Documentation

## Plot methylation profile from data

### Description

This function plots the low resolution profiles for all bisulfite sequencing data.

### Usage

    plotMethylationProfileFromData(methylationData1, methylationData2 = NULL,
      regions = NULL, conditionsNames = NULL, context = "CG",
      windowSize = NULL, autoscale = FALSE, labels = NULL, col = NULL,
      pch = c(1, 0, 16, 2, 15, 17), lty = c(4, 1, 3, 2, 6, 5),
      contextPerRow = TRUE)

### Arguments

`methylationData1` | the methylation data in condition 1 (see `methylationDataList`).
`methylationData2` | the methylation data in condition 2 (see `methylationDataList`). This is optional.
`regions` | a `GRanges` object with the regions where to plot the profiles.
`conditionsNames` | the names of the two conditions. This will be used to plot the legend.
`context` | a `vector` with all contexts in which the DMRs are computed (`"CG"`, `"CHG"` or `"CHH"`).
`windowSize` | a `numeric` value indicating the size of the window in which methylation is averaged.
`autoscale` | a `logical` value indicating whether the values are autoscalled for each context or not.
`labels` | a `vector` of `character` used to add a subfigure character to the plot. If `NULL` nothing is added.
`col` | a `character` vector with the colours. It needs to contain a minimum of 2 colours per condition. If not or if `NULL`, the defalut colours will be used.
`pch` | the R symbols used to plot the data It needs to contain a minimum of 2 symbols per condition. If not or if `NULL`, the defalut symbols will be used.
`lty` | the line types used to plot the data. It needs to contain a minimum of 2 line types per condition. If not or if `NULL`, the defalut line types will be used.
`contextPerRow` | a `logical` value indicating if the each row represents an individual context. If `FALSE`, each column will represent an individual context.

### Value

Invisibly returns `NULL`

### Author(s)

Nicolae Radu Zabet

### See Also

`plotMethylationProfile`, `computeMethylationProfile` and `methylationDataList`

### Examples

    # load the methylation data
    data(methylationDataList)

    #plot the low resolution profile at 10 Kb resolution
    par(mar=c(4, 4, 3, 1)+0.1)
    plotMethylationProfileFromData(methylationDataList[["WT"]],
                                   methylationDataList[["met1-3"]],
                                   conditionsNames=c("WT", "met1-3"),
                                   windowSize = 20000, autoscale = TRUE,
                                   context = c("CHG"))

    ## Not run:
    #plot the low resolution profile at 5 Kb resolution
    par(mar=c(4, 4, 3, 1)+0.1)
    plotMethylationProfileFromData(methylationDataList[["WT"]],
                                   methylationDataList[["met1-3"]],
                                   conditionsNames=c("WT", "met1-3"),
                                   windowSize = 5000, autoscale = TRUE,
                                   context = c("CG", "CHG", "CHH"),
                                   labels = LETTERS)

    ## End(Not run)

[Package DMRcaller version 1.14.2 Index]