RNA Velocity Ratio

Summarize spliced-to-unspliced ratios without claiming inferred latent time.

Description

Unspliced and spliced count ratios summarize transcript processing abundances.

Unspliced and spliced count ratios summarize transcript processing abundances. Such ratios alone do not infer RNA velocity or latent time.^[1]

Summarize spliced-to-unspliced ratios without claiming inferred latent time.

When to use RNA Velocity Ratio

Use this tool to summarize spliced-to-unspliced ratios without claiming inferred latent time.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use RNA Velocity Ratio and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter splicedCounts, unsplicedCounts, pseudocount using the field table and calculation rules, then run the tool.
Read unsplicedToSpliced, meanRatio. 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
splicedCounts	Spliced counts	list of number	Required
unsplicedCounts	Unspliced counts	list of number	Required
pseudocount	Pseudocount	number	Required

Enter aligned nonempty nonnegative count lists and a nonnegative pseudocount. Every adjusted spliced denominator must be positive. Return unspliced-to-spliced ratios and their arithmetic mean; the output direction is unspliced divided by spliced despite the broad metadata wording.

ratio_i=(unspliced_i+p)/(spliced_i+p)

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

Output field	Meaning	Value type
unsplicedToSpliced	Unspliced to spliced	list of number
meanRatio	Mean ratio	number

json

{
  "input": {
    "splicedCounts": [
      10,
      20
    ],
    "unsplicedCounts": [
      5,
      5
    ],
    "pseudocount": 0
  },
  "output": {
    "unsplicedToSpliced": [
      0.5,
      0.25
    ],
    "meanRatio": 0.375
  }
}

Limitations and assumptions

No kinetic model, neighborhood smoothing, uncertainty or velocity vector is fitted. The mean of per-feature ratios differs from a ratio of totals.

Numeric inputs 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 Transcripts Per Million: Normalize transcript length-adjusted abundances to one million TPM. For a complementary task, use Pseudotime Root Selector: Select the earliest cell as the pseudotime trajectory root.

References

RNA Velocity Ratio — tool.io

Similar or alternative tools

Transcripts Per Million
Normalize transcript length-adjusted abundances to one million TPM.
Pseudotime Root Selector
Select the earliest cell as the pseudotime trajectory root.