computeMethylationDataCoverage {DMRcaller} | R Documentation |
This function computes the coverage for bisulfite sequencing data. It
returns a vector
with the proportion (or raw count) of cytosines that
have the number of reads higher or equal than a vector
of specified
thresholds.
computeMethylationDataCoverage(methylationData, regions = NULL, context = "CG", breaks = NULL, proportion = TRUE)
methylationData |
the methylation data stored as a |
regions |
a |
context |
the context in which the DMRs are computed ( |
breaks |
a |
proportion |
a |
a vector
with the proportion (or raw count) of cytosines that
have the number of reads higher or equal than the threshold values specified
in the breaks
vector
.
Nicolae Radu Zabet and Jonathan Michael Foonlan Tsang
plotMethylationDataCoverage
,
methylationDataList
# load the methylation data data(methylationDataList) # compute coverage in CG context breaks <- c(1,5,10,15) coverage_CG_wt <- computeMethylationDataCoverage(methylationDataList[["WT"]], context="CG", breaks=breaks)