ABC Linkage Rank

Rank enhancer-gene links by activity-by-contact score.

Description

Activity-by-contact ranking normalizes supplied products, separately from a full gene-linking pipeline.

Activity-by-contact ranking normalizes supplied products, separately from a full gene-linking pipeline.^[1]

Rank enhancer-gene links by activity-by-contact score.

When to use ABC Linkage Rank

Use this tool to rank enhancer-gene links by activity-by-contact score.

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.

How to use ABC Linkage Rank and understand its results

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
Enter activities, contacts, targetIndex using the field table and calculation rules, then run the tool.
Read abcScores, targetRank. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
activities	Enhancer activities	list of number	Required
contacts	Enhancer contacts	list of number	Required
targetIndex	Target index	integer; minimum: 0	Required

Enter nonempty aligned finite lists with positive total and valid zero-based candidate index; return normalized scores and first-tied one-based rank.

raw=activity×contact; normalized=raw/sum(raw)

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
abcScores	Normalized ABC scores	list of number
targetRank	Target rank	integer; minimum: 1

json

{
  "input": {
    "activities": [
      1,
      2,
      1
    ],
    "contacts": [
      1,
      1,
      3
    ],
    "targetIndex": 2
  },
  "output": {
    "abcScores": [
      0.16666666666666666,
      0.3333333333333333,
      0.5
    ],
    "targetRank": 1
  }
}

Limitations and assumptions

Signed inputs allow negative scores or values above one. No enhancer calling, contact processing or gene assignment is performed.

Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Super-Enhancer Stitching: Stitch enhancer intervals separated by a supplied maximum distance. For a complementary task, use Promoter–Enhancer State: Resolve promoter-enhancer state from H3K4 methylation signals.

References

ABC Linkage Rank — tool.io

Similar or alternative tools

Super-Enhancer Stitching
Stitch enhancer intervals separated by a supplied maximum distance.
Promoter–Enhancer State
Resolve promoter-enhancer state from H3K4 methylation signals.