plotMethylationDataSpatialCorrelation {DMRcaller} | R Documentation |
This function plots the correlation of methylation levels for Cytosines located at a certain distance apart.
plotMethylationDataSpatialCorrelation(methylationData1, methylationData2 = NULL, distances, regions = NULL, conditionsNames = NULL, context = "CG", labels = NULL, col = NULL, pch = c(1, 0, 16, 2, 15, 17), lty = c(4, 1, 3, 2, 6, 5), contextPerRow = FALSE, log = "")
methylationData1 |
the methylation data in condition 1
(see |
methylationData2 |
the methylation data in condition 2
(see |
distances |
a |
regions |
a |
conditionsNames |
a vector of character with the names of the conditions
for |
context |
the context in which the DMRs are computed ( |
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 |
log |
a |
This function plots the proportion of cytosines in a specific context that have at least a certain number of reads (x-axis)
Invisibly returns NULL
Nicolae Radu Zabet
computeMethylationDataSpatialCorrelation
,
methylationDataList
## Not run: # load the methylation data data(methylationDataList) # plot the spatial correlation in CG context par(mar=c(4, 4, 3, 1)+0.1) plotMethylationDataSpatialCorrelation(methylationDataList[["WT"]], distances = c(1,5,10,15), regions = NULL, conditionsNames = c("WT","met1-3"), context = c("CG"), labels = LETTERS, col = NULL, pch = c(1,0,16,2,15,17), lty = c(4,1,3,2,6,5), contextPerRow = FALSE) # plot the spatial correlation in all three contexts plotMethylationDataSpatialCorrelation(methylationDataList[["WT"]], methylationDataList[["met1-3"]], distances = c(1,5,10,15,20,50,100,150,200,500,1000), regions = NULL, conditionsNames = c("WT","met1-3"), context = c("CG", "CHG", "CHH"), labels = LETTERS, col = NULL, pch = c(1,0,16,2,15,17), lty = c(4,1,3,2,6,5), contextPerRow = FALSE, log="x") ## End(Not run)