This would create a sparse track of the form "track_prefix.mcmetacell" for each metacell in the McCounts object. The counts are smoothed by a running sum window of size window_size * 2 + 1 (default: 201).
The resulted track would be stored in a 'dense' format with a resolution of resolution bp (default: 10).
Each track would have a track attribute named "total_cov" with the total coverage of the metacell.
If create_marginal_track is TRUE (default), an additional track with the total counts over all the metacells will be created.
Counts can be normalized to the total counts of each metacell by setting normalize = TRUE.
Usage
mcc_to_tracks(
mc_counts,
track_prefix,
metacells = NULL,
overwrite = FALSE,
resolution = 20,
window_size = NULL,
create_marginal_track = TRUE,
normalize = FALSE
)Arguments
- mc_counts
A McCounts object
- track_prefix
The prefix of the tracks to create (i.e. misha directory). Track names will be of the form "track_prefix.mcmetacell"
- metacells
metacells for which to create tracks. If NULL, all metacells will be used.
- overwrite
Whether to overwrite existing tracks.
- resolution
The resolution of each track (default: 20bp)
- window_size
The size of the window used to smooth the counts. The counts of at position i are smoothed by a sum of the counts of i - window_size, i + window_size. If NULL - the counts are not smoothed.
- create_marginal_track
Create a track with the total counts from all the metacells. The track would be named "track_prefix.marginal"
- normalize
Normalize each metacell by the sum of its counts.