Extracts patterns given pattern space
gpatterns.tidy_cpgs_to_pats(track, pattern_space = NULL,
pattern_space_file = NULL, max_missing = Inf, min_cov = 1,
by_coord_bin = TRUE, parallel = getOption("gpatterns.parallel"), ...)
Arguments
- track
- name of track
- pattern_space
- pattern space data frame
(output of gpatterns.tracks_to_pat_space or gpatterns.intervs_to_pat_space)
needs to have the following fields: chrom,start,end,fid
- pattern_space_file
- file that holds the pattern space
- max_missing
- maximal number of missing data ('*') in pattern
- min_cov
- minimal pattern coverage
- by_coord_bin
- execute separatly for each coordinates bin
(for tracks that do not fit into memory)
- ...
- additional parameters to gpatterns.apply_tidy_cpgs