makeMethPlot: Create methylation region plot

In jmacdon/methylation: Package to analyze methylation data from Illumina 450K arrays

Description

Create a plot for a region showing differential methylation.

Usage

makeMethPlot(bumpsObj, eset, row, txdb, orgpkg, samps, dontuse = "",
  stratifyBySex = FALSE, sexfirst = "Male", use.symbols = TRUE,
  fitobj = NULL, linearfit = FALSE, coefcol = NULL)

Arguments

bumpsObj	The output from bumphunter
eset	Usually a GenomicRatioSet created by the minfi package
row	Which row of the bumpsObj are we plotting?
txdb	A transcript database object (e.g., TxDb.Hsapiens.UCSC.hg19.knownGene)
orgpkg	A species-level annotation package (e.g., Homo.sapiens)
samps	A data.frame containing sample information. This data.frame must contain two columns; one called Gender, listing the gender of each sex, and one called Category, listing the category for each sample
dontuse	A character vector of Category levels that won't be plotted. If using all levels, this argument is "".
stratifyBySex	Boolean. Should we plot the data stratified by sex?
sexfirst	Which sex should be plotted first? In general this is the sex for which the bump being shown was significant. Only used if stratifyBySex is TRUE.
use.symbols	Should we convert transcript IDs to gene symbols?
fitobj	An MArrayLM object, after fitting the same model as bumphunter. This is the source of the methylation data in the plot
linearfit	Boolean. Are we fitting a continuous covariate TRUE or ANOVA FALSE. Defaults to FALSE.
coefcol	If a linear fit, which coefficient of the fitobj is the slope?

Details

This function is used to plot a genomic region where there is differential methylation that includes the methylation data, a smoothed line, and any genes in the region. This function is in general not called by the end user. Instead use methByRegion.

Value

This function doesn't return anything. It is only called for the side effect of creating a plot.

Author(s)

James W. MacDonald ([e-mail])

jmacdon/methylation documentation built on May 19, 2019, 12:49 p.m.