Description Usage Arguments Details Author(s) See Also Examples

Plot differentially methylated regions (DMRs) from tiling microarray data that were identified using the dmrFind function.

1 | ```
plotDMRs(dmrs, Genome, cpg.islands, exposure, outfile, which_plot=1:50, which_lines=NULL, which_points=which_lines, ADD=3000, cols=c("black","blue","red","gray","brown","pink","orange"), legend.size=1, smoo="loess", SPAN=300, DELTA=36, point.info=FALSE, pch.groups=NULL, panel3="pvalues", G=NULL, seq=NULL)
``` |

`dmrs` |
a list object as returned by dmrFind. |

`Genome` |
the BSgenome object for the organism based upon which your array was designed. |

`cpg.islands` |
a table with columns "chr","start", and "end" for CpG islands to plot in the second panel. |

`exposure` |
The covariate of interest. |

`outfile` |
the name of the file to save (including the full path) |

`which_plot` |
numeric vector of indices identifying which DMR candidates from dmrs$dmrs to plot. |

`which_lines` |
vector specifying which groups (unique elements of exposure) to plot the lines for. If NULL (the default), plots lines for all groups. Only applies if exposure is categorical. |

`which_points` |
vector specifying which groups (unique elements of exposure) to plot the points for. If NULL (the default), plots points for all groups. Only applies if exposure is categorical. |

`SPAN` |
see DELTA. Only used if smoo="loess" |

`DELTA` |
span parameter in loess smoothing will = SPAN/(DELTA * number of probes in the plotted region). Only used if smoo="loess". |

`smoo` |
"loess" for loess smoother or "runmed" for running median smoother (runmed with k=3). This does not need to be the same as the smoo argument to dmrFind. |

`ADD` |
Number of base pairs to plot on either side of each DMR candidate (if it is covered on the array). |

`cols` |
vector of colors to use, one for each group (if covariate is categorical) |

`point.info` |
if TRUE, function returns a table identifying which sample is plotted with which number or letter (if pch.groups=NULL, the default). |

`legend.size` |
magnification factor for the legend |

`pch.groups` |
vector whose length is equal to the number of samples. Each unique value will be plotted with a different point type. |

`panel3` |
if panel3="G", the third panel of each DMR plot will show the difference between the median green channel value (after subtracting probe medians and correcting for gc content) between the 2 groups (i.e., the group defined by mod[,coef] in dmrFind minus the reference group). If panel="G", seq argument must be provided. If panel!="G", the 3rd panel will show -log10(dmrs$pval). G |

`G` |
matrix of green channel intensities to use for plotting in the 3rd panel if panel3="G". |

`seq` |
vector of probe sequences corresponding to the rows of G (and dmrs$cleanp) if panel3="G". |

This function plots the differentially methylated regions (DMRs) that were identified using the dmrFind function.

Martin Aryee <[email protected]>, Peter Murakami, Rafael Irizarry

1 | ```
# See qval
``` |

Bioconductor-mirror/charm documentation built on June 1, 2017, 5:29 a.m.

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