Generate pattern space for specific genomic loci
gpatterns.intervs_to_pat_space(tracks, intervals, pat_len, adjacent = TRUE,
add_rest = FALSE, min_cov = 1, max_span = 500,
expand_intervals = FALSE,
nchunks = getOption("gpatterns.parallel.thread_num"),
parallel = getOption("gpatterns.parallel"), verbose = FALSE)
Arguments
- tracks
- tracks
- intervals
- genomic loci to cover (chrom,start,end), with an optional field
'fid'.
- pat_len
- pattern length
- adjacent
- generate patterns that do not skip a CpG
- add_rest
- add rest of the genome (using gpatterns.tracks_to_pat_space)
- min_cov
- if adjacent: minimal pattern coverage for interval. else - minimal CpG coverage
- max_span
- maximum span to look for CpGs
- expand_intervals
- expand intervals by max_span when intervals are single CpG loci
- nchunks
- override global gpatterns.parallel.thread_num definition
- parallel
- override global gpatterns.parallel definition
- verbose
- print additional progress messages