gextract methylation data

gextract_meth(
  tracks,
  names = NULL,
  intervals = gintervals.all(),
  iterator = "intervs.global.seq_CG",
  d_expand = NULL,
  join_intervals = FALSE,
  extract_meth_calls = FALSE,
  avg_tracks = NULL,
  avg_tracks_names = NULL,
  annot_tracks = NULL,
  annot_tracks_names = NULL,
  min_cov = NULL,
  ...
)

Arguments

tracks: name of methylation track suffix (without ".cov" or ".meth")
names: sets the columns names in the returned value.
intervals: genomic scope for which the function is applied
iterator: track expression iterator. If "NULL" iterator is based on CpGs
d_expand: smooth the methylation signal d_expand bp from each side (optional).
join_intervals: add the intervals to the returned data frame (using left_join)
extract_meth_calls: extract also methylation calls (".meth" tracks)
avg_tracks: tracks of average methylation (for tracks that do not have ".cov" and ".meth" tracks)
avg_tracks_names: names of tracks in avg_tracks (optional)
annot_tracks: other tracks to extract
annot_tracks_names: names of annotation tracks
min_cov: minimal coverage per track. If the coverage is below this number the methylation values would be changed to NA.
...: additional arguments to gextract

Value

data frame with a column with average methylation for each track, and another column with ".cov" suffix with every track's coverage. If extract_meth_calls is TRUE - additional columns with ".meth" suffix with number of methylation calls per track.

gextract methylation data

Arguments

Value

See also