Returns the example misha database — shaman_get_test_track

shaman_get_test_track_db Returns the path of an example misha database with Hi-C contacts from the ELA K562 dataset.

shaman_get_test_track_db(full = FALSE)

Arguments

full: Whether to return the full example database (downloaded on first use) instead of the small one.

Value

The path of the database.

Details

By default this is a small database that is built in the session's temporary directory on first use; later calls in the session reuse it. It has one chromosome (hg19 chr2) and the observed (hic_obs), expected (hic_exp) and score (hic_score) tracks of chr2:176.5e06-177e06, around the hoxd locus (46,735 observed contacts, each stored in both orientations).

With full = TRUE it returns the full example database of earlier shaman versions: 4.6 million contacts from the ELA K562 dataset covering the hoxd locus (chr2:175e06-178e06) and convergent CTCF regions, with scores for chr2:175e06-178e06. It is downloaded (about 100MB, from the lab's public S3 bucket) and extracted into the user cache directory (tools::R_user_dir("shaman", "cache"), about 480MB) on first use; later calls reuse it. Processing the complete matrix from this study requires downloading the full contact list and regenerating the reshuffled matrix.

Examples

library(misha)
gsetroot(shaman_get_test_track_db())
gtrack.ls()
#> [1] "hic_exp"   "hic_obs"   "hic_score"