Get fragment coverage — gpatterns.get_fragment_cov • gpatterns

get number of molecules per each fragment for a track. This can give us some upper bound of the number of methylation patterns per fragment.

gpatterns.get_fragment_cov(track, intervals = NULL, save_track = FALSE,
  parallel = getOption("gpatterns.parallel"), ...)

Arguments

track: track
intervals: fragment intervals. if NULL - fragments would be based chrom,start,end positions of tidy_cpgs, assuming gpatterns.adjust_read_pos was called before (as in any run of gpatterns.import_* with frag_intervs parameter).
parallel: parallel
...: other parameters of gpatterns.adjust_read_pos

Value

data frame with fragmets coordinates (chrom,start,end) and 'frag_cov' field with the fragment coverage