Set genomic features in ChromatinContacts object

Assigns or updates genomic features (TADs, loops, compartments, tracks) in a ChromatinContacts object. Features are automatically subsetted to overlap with loaded interactions, ensuring only relevant data is retained.

Usage

features(x, name, ...) <- value

# S4 method for class 'ChromatinContacts,character,GRanges'
features(x, name, ...) <- value

# S4 method for class 'ChromatinContacts,character,GInteractions'
features(x, name, ...) <- value

# S4 method for class 'ChromatinContacts,character,GRangesList'
features(x, name, ...) <- value

# S4 method for class 'ChromatinContacts,character,list'
features(x, name, ...) <- value

Arguments

x

ChromatinContacts object with imported interaction data.

name

Character. Feature slot name:

• "compartments": A/B compartment annotations (GRanges)

• "TADs": Topologically associating domains (GRanges)

• "multi_contacts": Multi-way contact regions (GRanges)

• "loops": Chromatin loop calls (GInteractions)

• "tracks": Genomic signal tracks (GRangesList)

...

Additional arguments (not currently used).

value

Feature data with appropriate type:

• GRanges: for compartments, TADs, multi_contacts

• GInteractions: for loops

• GRangesList or list: for tracks (will be converted to GRangesList)

Value

ChromatinContacts object with updated features slot. The modified object is returned invisibly to support piping.

Details

Requirements

Interactions must be imported before assigning features. Use import() first.

Automatic subsetting

Features are automatically filtered to retain only elements overlapping the loaded Hi-C interaction data. This prevents visualization errors and reduces memory usage.

Track naming

When providing tracks as GRangesList, ensure they are named for proper labeling in plots. Unnamed tracks receive default names (track1, track2, etc.).

See also

features(), ChromatinContacts(), import-ChromatinContacts

Examples

if (FALSE) { # \dontrun{
# Load Hi-C data first
cc <- ChromatinContacts("sample.cool") |> import()

# Add TADs from BED file
features(cc, "TADs") <- rtracklayer::import("TADs.bed")

# Add chromatin loops
features(cc, "loops") <- loops_ginteractions

# Add multiple ChIP-seq tracks
features(cc, "tracks") <- GRangesList(
  H3K27ac = rtracklayer::import("H3K27ac.bw"),
  H3K4me3 = rtracklayer::import("H3K4me3.bw")
)

# Add compartments
features(cc, "compartments") <- compartment_gr

# Chain operations
cc <- ChromatinContacts("sample.cool") |>
  import() |>
  `features<-`("TADs", value = tads) |>
  `features<-`("loops", value = loops)
} # }