get_track_defaults: Get UCSC track default values and track templates

In jmw86069/platjam: Platform Jam, biological platform importers.

Get UCSC track default values and track templates

Description

Get UCSC track default values and track templates

Usage

get_track_defaults(env = new.env())

Arguments

env

environment in which to store the default values and track templates. If the input env already contains any of the environment names, they will be used as-is without modification. Therefore, to use custom default values, or a custom template: call default_env <- get_track_defaults() edit the environment, call parse_ucsc_gokey(..., default_env=default_env) Relevant default values are stored in these list elements: composite_bed_defaults composite_defaults overlay_defaults

Details

This function defines default values for overlay and composite track types. It also defines three templates each for overlay and composite:

• overlay_header - equivalent to superTrack

• overlay_parent - equivalent to one set of overlay tracks

• overlay_track - each overlay track

• composite_header - equivalent to one composite track

• composite_parent - equivalent to a composite view within a composite track

• composite_track - individual track within the composite track.

Value

environment which contains each template chunk for each type of track section, and the corresponding default values.

See Also

Other jam ucsc browser functions: assign_track_defaults(), make_ucsc_trackname(), parse_ucsc_gokey()

Examples

default_env <- get_track_defaults();
# describe the contents
jamba::sdim(default_env)

# customize view default to "PEAKS" instead of "JUNC"
default_env$composite_bed_defaults$view <- "PEAKS"
# change type to bigBed 10
default_env$composite_bed_defaults$type <- "bigBed 10"
data.frame(composite_bed_defaults=unlist(default_env$composite_bed_defaults))

# customize multiWig aggregate to "none"
default_env$overlay_defaults$aggregate <- "none";

jmw86069/platjam documentation built on Sept. 26, 2024, 3:31 p.m.