gextract_meth: gextract methylation data

In tanaylab/misha.ext: A home to functions that extend the misha package

gextract methylation data

Description

gextract methylation data

Usage

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.

See Also

gextract

tanaylab/misha.ext documentation built on Oct. 1, 2024, 10:55 a.m.