Convert 2D track to indexed format

Converts a per-chromosome-pair 2D track (rectangles or points) to indexed format (track.dat + track.idx). This reduces file descriptor usage from O(N^2) to O(1), which is especially beneficial for genomes with many contigs.

gtrack.2d.convert_to_indexed(track = NULL, remove.old = FALSE, force = FALSE)

Arguments

track

track name to convert

remove.old

Logical. If TRUE, removes old per-chromosome-pair files after successful conversion. Default: FALSE.

force

Logical. If TRUE, re-converts even if already in indexed format. Default: FALSE.

Value

None.

See also

gtrack.2d.create, gtrack.2d.import, gtrack.2d.import_contacts, gtrack.convert_to_indexed, gdb.convert_to_indexed

Examples

if (FALSE) { # \dontrun{
# Convert a 2D track to indexed format
gtrack.2d.convert_to_indexed("my_2d_track")

# Convert and remove old per-pair files
gtrack.2d.convert_to_indexed("my_2d_track", remove.old = TRUE)

# Force re-conversion
gtrack.2d.convert_to_indexed("my_2d_track", force = TRUE)
} # }