plotMethylationProfileFromData {DMRcaller} | R Documentation |
This function plots the low resolution profiles for all bisulfite sequencing data.
plotMethylationProfileFromData(methylationData1, methylationData2 = NULL, regions = NULL, conditionsNames = NULL, context = "CG", windowSize = NULL, autoscale = FALSE, labels = NULL, col = NULL, pch = c(1, 0, 16, 2, 15, 17), lty = c(4, 1, 3, 2, 6, 5), contextPerRow = TRUE)
methylationData1 |
the methylation data in condition 1
(see |
methylationData2 |
the methylation data in condition 2
(see |
regions |
a |
conditionsNames |
the names of the two conditions. This will be used to plot the legend. |
context |
a |
windowSize |
a |
autoscale |
a |
labels |
a |
col |
a |
pch |
the R symbols used to plot the data It needs to contain a minimum
of 2 symbols per condition. If not or if |
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 |
contextPerRow |
a |
Invisibly returns NULL
Nicolae Radu Zabet
plotMethylationProfile
,
computeMethylationProfile
and methylationDataList
# load the methylation data data(methylationDataList) #plot the low resolution profile at 10 Kb resolution par(mar=c(4, 4, 3, 1)+0.1) plotMethylationProfileFromData(methylationDataList[["WT"]], methylationDataList[["met1-3"]], conditionsNames=c("WT", "met1-3"), windowSize = 20000, autoscale = TRUE, context = c("CHG")) ## Not run: #plot the low resolution profile at 5 Kb resolution par(mar=c(4, 4, 3, 1)+0.1) plotMethylationProfileFromData(methylationDataList[["WT"]], methylationDataList[["met1-3"]], conditionsNames=c("WT", "met1-3"), windowSize = 5000, autoscale = TRUE, context = c("CG", "CHG", "CHH"), labels = LETTERS) ## End(Not run)