splitDataByGRanges  R Documentation 
This function splits the methylation data into regions based on the genomic annotations provided under the form of a GenomicRanges object.
splitDataByGRanges( dat, chr, annots, gap = 1, min.cpgs = 50, max.cpgs = 2000, verbose = TRUE )
dat 
a data frame with rows as individual CpGs appearing
in all the samples. The first 4 columns should contain the information of

chr 
character vector containing the chromosome information. Its length
should be equal to the number of rows in 
annots 
GenomicRanges object containing the annotations 
gap 
integer defining the maximum gap that is allowed between
two regions to be considered as overlapping.
According to the 
min.cpgs 
positive integer defining the minimum number of CpGs within a region for the algorithm to perform optimally. The default value is 50. 
max.cpgs 
positive integer defining the maximum number of CpGs within a region for the algorithm to perform optimally. The default value is 2000. 
verbose 
logical indicates if the algorithm should provide progress report information. The default value is TRUE. 
A named list
of data.frame
containing the data of each
independent region.
Audrey Lemaçon
## data(RAdat) RAdat.f < na.omit(RAdat[RAdat$Total_Counts != 0, ]) annot < GenomicRanges::GRanges(seqnames = "chr1", IRanges::IRanges( start = c(102711720,102711844,102712006,102712503,102712702), end = c(102711757,102711909,102712195,102712637,102712712) )) results < splitDataByGRanges(dat = RAdat.f, chr = rep(x = "chr1", times = nrow(RAdat.f)), annots = annot, gap = 1, min.cpgs = 5)
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