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crazyhottommy/tile_chromHMM_segments.md

Created March 6, 2018 17:52
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tile_chromHMM_segments.md

When call chromHMM with a bin size of say 1000 bp, if the consecutive bins are of the same state, it will be merged.

I want to tile the segment file before merging. https://support.bioconductor.org/p/102775/#102777

library(GenomicRanges)
library(rtracklayer)
chromHMM_seg<- import("data/chromHMM/SKCM-M852-P008_18_segments.bed", format = "BED")

chromHMM_seg_tile<- tile(chromHMM_seg, width = 1000)
names(chromHMM_seg_tile)<- chromHMM_seg$name
stack(chromHMM_seg_tile, "state")
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