Make Rle from segments for one sample
Take output of CBS, make Rle representing all features in 'locs' ranges. CBS output contains run length and run values for genomic segmetns, which could very directly be converted into a Rle. However, as NA values are often removed, especially for mBAF data, these run lengths do not necessarily cover all features in every sample. Using the start and top positions of each segment and the location of each feature, we can make a Rle that represents all features.
data.frame of segments, formatted as output of segment function from DNAcopy package
GenomicRanges, like rowRanges slot of a GenoSet
Rle with run lengths and run values covering all features in the data set.
Other "segmented data":
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