plotMethylationDataCoverage: Plot methylation data coverage

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/coverage.R

Description

This function plots the coverage for the bisulfite sequencing data.

Usage

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plotMethylationDataCoverage(methylationData1, methylationData2 = NULL, breaks,
  regions = NULL, conditionsNames = NULL, context = "CG",
  proportion = TRUE, labels = NULL, col = NULL, pch = c(1, 0, 16, 2, 15,
  17), lty = c(4, 1, 3, 2, 6, 5), contextPerRow = FALSE)

Arguments

methylationData1

the methylation data in condition 1 (see methylationDataList).

methylationData2

the methylation data in condition 2 (see methylationDataList). This is optional.

breaks

a numeric vector specifing the different values for the thresholds when computing the coverage.

regions

a GRanges object with the regions where to compute the coverage. If NULL, the coverage is computed genome-wide.

conditionsNames

a vector of character with the names of the conditions for methylationData1 and methylationData2.

context

the context in which the DMRs are computed ("CG", "CHG" or "CHH").

proportion

a logical value indicating whether proportion or counts will be plotted.

labels

a vector of character used to add a subfigure character to the plot. If NULL nothing is added.

col

a character vector with the colors. It needs to contain a minimum of 2 colors per condition. If not or if NULL, the defalut colors will be used.

pch

the R symbols used to plot the data. It needs to contain a minimum of 2 symbols per condition. If not or if NULL, the defalut symbols will be used.

lty

the line types used to plot the data. It needs to contain a minimum of 2 line types per condition. If not or if NULL, the defalut line types will be used.

contextPerRow

a logical value indicating if the each row represents an individual context. If FALSE, each column will represent an individual context.

Details

This function plots the proportion of cytosines in a specific context that have at least a certain number of reads (x-axis)

Value

Invisibly returns NULL

Author(s)

Nicolae Radu Zabet

See Also

computeMethylationDataCoverage, methylationDataList

Examples

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# load the methylation data
data(methylationDataList)

# plot the coverage in CG context
par(mar=c(4, 4, 3, 1)+0.1)
plotMethylationDataCoverage(methylationDataList[["WT"]],
                           methylationDataList[["met1-3"]],
                           breaks = c(1,5,10,15), regions = NULL,
                           conditionsNames = c("WT","met1-3"),
                           context = c("CG"), proportion = TRUE,
                           labels = LETTERS, col = NULL,
                           pch = c(1,0,16,2,15,17), lty = c(4,1,3,2,6,5),
                           contextPerRow = FALSE)

## Not run: 
# plot the coverage in all three contexts
plotMethylationDataCoverage(methylationDataList[["WT"]],
                           methylationDataList[["met1-3"]],
                           breaks = 1:15, regions = NULL,
                           conditionsNames = c("WT","met1-3"),
                           context = c("CG", "CHG", "CHH"),
                           proportion = TRUE, labels = LETTERS, col = NULL,
                           pch = c(1,0,16,2,15,17), lty = c(4,1,3,2,6,5),
                           contextPerRow = FALSE)

## End(Not run)

nrzabet/DMRcaller documentation built on May 23, 2019, 2:50 p.m.