plotRegion: Plot results in a genomic region

In isglobal-brge/MEAL: Perform methylation analysis and facilitates differential expression analyses

Description

Plot the results from the different analyses of a ResultSet in a specific genomic region. It can plot all the results from runPipeline.

Usage

plotRegion(
  rset,
  range,
  results = names(rset),
  genome = "hg19",
  rset2,
  tPV = 5,
  fNames = c("chromosome", "start", "end"),
  fNames2 = c("chromosome", "start", "end")
)

Arguments

rset	ResultSet
range	GenomicRanges with the region coordinates
results	Character with the analyses that will be included in the plot. By default, all analyses available are included.
genome	String with the genome used to retrieve transcripts annotation: hg19, hg38, mm10. (Default: "hg19")
rset2	Additional ResultSet
tPV	Threshold for P-Value
fNames	Names from rset fData
fNames2	Names from rset2 fData

Details

This plot allows to have a quick summary of the methylation or gene expression analyses in a given region. If we use a ResultSet obtained from methylation data, transcripts annotation is obtained from archive. If we use a ResultSet obtained from gene expression data, transcripts annotation is taken from fData.

This plot can be used to plot the results of one dataset (methylation or gene expression) or to represent the association between methylation and gene expression data. If only one dataset is used, the p-values and the coefficients of DiffMean and DiffVar analyses are plotted. If we pass two ResultSets, rset should contain methylation results and a rset2 the gene expression results.

Value

Regional plot

isglobal-brge/MEAL documentation built on May 8, 2021, 8:05 p.m.