metBoxPlot: scatter.plot to plot scatter plots between gene expression...

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

scatter.plot is a function to plot various scatter plots between gene expression and DNA methylation. When byPair is specified, scatter plot for individual probe-gene pairs will be generated. When byProbe is specified, scatter plots for one probes with nearby 20 gene pairs will be generated. When byTF is specified, scatter plot for TF expression and average DNA methylation at certain motif sites will be generated.

Usage

metBoxPlot(
  data,
  group.col,
  group1,
  group2,
  probe,
  min.samples = 5,
  minSubgroupFrac = 0.2,
  diff.dir = "hypo",
  legend.col = NULL,
  title = NULL,
  filename = NULL,
  save = TRUE
)

Arguments

data	A multiAssayExperiment with DNA methylation and Gene Expression data. See createMAE function.
group.col	A column defining the groups of the sample. You can view the available columns using: colnames(MultiAssayExperiment::colData(data)).
group1	A group from group.col. ELMER will run group1 vs group2. That means, if direction is hyper, get probes hypermethylated in group 1 compared to group 2.
group2	A group from group.col. ELMER will run group1 vs group2. That means, if direction is hyper, get probes hypermethylated in group 1 compared to group 2.
probe	Character with probe name (i.e. "cg24517858")
min.samples	Minimun number of samples to use in the analysis. Default 5. If you have 10 samples in one group, percentage is 0.2 this will give 2 samples in the lower quintile, but then 5 will be used.
minSubgroupFrac	A number ranges from 0 to 1 specifying the percentage of samples from group1 and group2 that are used to identify the differential methylation. Default is 0.2 because we did not expect all cases to be from a single molecular subtype.But, If you are working with molecular subtypes please set it to 1.
diff.dir	A character can be "hypo" or "hyper", showing differential methylation dirction. It can be "hypo" which is only selecting hypomethylated probes; "hyper" which is only selecting hypermethylated probes;
legend.col	legend title
title	plot title
filename	File names (.png) to save the file (i.e. "plot.png")
save	Save plot as PNG

Value

Box plot

Author(s)

Tiago Chedraoui Silva (tiagochst at gmail.com)

Examples

## Not run: 
  data <- ELMER:::getdata("elmer.data.example")
  group.col <- "subtype_Expression.Subtype"
  group1 <- "classical"
  group2 <- "secretory"
  metBoxPlot(data,
             group.col = group.col,
             group1 = group1,
             group2 = group2, 
             probe ="cg17898069",
             minSubgroupFrac = 0.2, 
             diff.dir = "hypo")

## End(Not run)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.