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Compute Motif-Based DMR Interactions

Source: R/dmrs_interaction.R
computeDMRsInteraction.Rd

Computes motif-based interactions between DMRs based on their motif similarity. Identifies pairs of DMRs with significant motif similarity and returns a data frame of interactions. Assigns directionality based on score, if available.

Usage

computeDMRsInteraction(
  dmrs,
  genome = NULL,
  array = NULL,
  min_similarity = getOption("CMEnt.min_motif_similarity", 0.8),
  beta_locs = NULL,
  motif_site_flank_size = 5,
  find_components = TRUE,
  min_component_size = 2,
  query_components_with_jaspar = TRUE,
  plot_dir = NULL,
  output_prefix = NULL
)

Arguments

dmrs

Dataframe or GRanges object containing DMR coordinates and motif information

genome

Character. Genome version to use for sequence extraction. Required for data.frame DMRs; inferred from GRanges seqinfo when available.

array

Character. Array platform type (e.g., "450K", "EPIC"). Required only when beta_locs is not provided and DMR site IDs are array probe IDs.

min_similarity

Numeric. Minimum motifs PWM similarity threshold for considering DMRs are related (default: 0.8)

beta_locs

Data frame. Optional pre-computed genomic locations. If NULL, locations will be retrieved using getSortedGenomicLocs (default: NULL)

motif_site_flank_size

Integer. Number of base pairs to include as flanking regions around each site site (default: 5)

find_components

Logical. Whether to identify connected components of interacting DMRs (default: TRUE)

min_component_size

Integer. Minimum size of connected components to consider (default: 2)

query_components_with_jaspar

Logical. Whether to query connected components average PWMs against JASPAR database (default: TRUE)

plot_dir

Character. Directory to save diagnostic plots (optional). If NULL, no plots are saved (default: NULL)

output_prefix

Character. Prefix for output files to save interactions and components (optional). If NULL, results are not saved to file (default: NULL)

Value

A list with:

  • interactions: Data frame of motif-based DMR interactions with columns chr1, start1, end1, chr2, start2, end2, sim, and when components are requested, component_id

  • components: Data frame of discovered motif components

  • dmrs: The input DMRs in the same class as provided, with an added component_ids column containing comma-separated component IDs for each DMR (or NA when the DMR is not part of a retained component)

Examples

# Compute motif-based interactions for DMRs
dmrs <- data.frame(
    chr = c("chr16", "chr3"),
    start = c(53468112, 37459206),
    end = c(53468712, 37493431),
    start_site = c("cg00000029", "cg00000108"),
    start_seed = c("cg00000029", "cg00000108"),
    end_site = c("cg13426503", "cg08730726"),
    end_seed = c("cg13426503", "cg08730726"),
    seeds = c("cg00000029,cg13426503", "cg00000108,cg08730726")
)
dmrs_with_motifs <- extractDMRMotifs(dmrs, genome = "hg19", array = "450K")
interactions <- computeDMRsInteraction(
    dmrs_with_motifs,
    genome = "hg19",
    array = "450K",
    query_components_with_jaspar = FALSE
)