makeMethPlot: Create methylation region plot

Description Usage Arguments Details Value Author(s)

Description

Create a plot for a region showing differential methylation.

Usage

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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 ([email protected])


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