analyseReadsInsideRegionsForCondition: Analyse reads inside regions for condition
In DMRcaller: Differentially Methylated Regions caller

Description Usage Arguments Value Author(s) See Also Examples

This function extracts from the methylation data the total number of reads, the number of methylated reads and the number of cytosines in the specific context from a region (e.g. DMRs)

1 2	analyseReadsInsideRegionsForCondition(regions, methylationData, context, label = "", cores = 1)

`regions`	a `GRanges` object with a list of regions on the genome; e.g. could be a list of DMRs
`methylationData`	the methylation data in one condition (see `methylationDataList`).
`context`	the context in which to extract the reads (`"CG"`, `"CHG"` or `"CHH"`).
`label`	a string to be added to the columns to identify the condition
`cores`	the number of cores used to compute the DMRs.

a GRanges object with additional four metadata columns

sumReadsM: the number of methylated reads
sumReadsN: the total number of reads
proportion: the proportion methylated reads
cytosinesCount: the number of cytosines in the regions

Nicolae Radu Zabet

filterDMRs, computeDMRs, DMRsNoiseFilterCG, and mergeDMRsIteratively

# load the methylation data
data(methylationDataList)

#load the DMRs in CG context. These DMRs were computed with minGap = 200.
data(DMRsNoiseFilterCG)

#retrive the number of reads in CHH context in WT
DMRsNoiseFilterCGreadsCHH <- analyseReadsInsideRegionsForCondition(
                             DMRsNoiseFilterCG[1:10],
                             methylationDataList[["WT"]], context = "CHH",
                             label = "WT")