Probe Risk Filter

Filter probes against caller-supplied SNP-affected and cross-reactive ID lists.

Description

Probe-risk exclusion depends on the supplied cross-reactivity and variant annotations.

Probe-risk exclusion depends on the supplied cross-reactivity and variant annotations.^[1]

Filter probes against caller-supplied SNP-affected and cross-reactive ID lists.

When to use Probe Risk Filter

Use this tool to filter probes against caller-supplied SNP-affected and cross-reactive ID lists.

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 Probe Risk Filter 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 probeIds, crossReactiveIds, snpAffectedIds using the field table and calculation rules, then run the tool.
Read retainedIds, flaggedIds, retainedPercent. 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
probeIds	Probe ids	list of string	Required
crossReactiveIds	Cross reactive ids	list of string	Required
snpAffectedIds	Snp affected ids	list of string	Required

Enter nonempty probe IDs and two risk lists; match exact case-sensitive untrimmed strings. Preserve order/duplicates and return retained percentage by entry count.

excluded=ID in union of risk lists

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

Output field	Meaning	Value type
retainedIds	Retained ids	list of string
flaggedIds	Flagged ids	list of string
retainedPercent	Retained percent	number

json

{
  "input": {
    "probeIds": [
      "a",
      "b",
      "c"
    ],
    "crossReactiveIds": [
      "b"
    ],
    "snpAffectedIds": [
      "c"
    ]
  },
  "output": {
    "retainedIds": [
      "a"
    ],
    "flaggedIds": [
      "b",
      "c"
    ],
    "retainedPercent": 33.33333333333333
  }
}

Limitations and assumptions

No sequences, genome build or variant database are checked.

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 Probe Pvalue Filter: Exclude methylation probes failing a detection p-value threshold. For a complementary task, use Blacklist Overlap Filter: Exclude genomic intervals that overlap caller-supplied blacklist intervals.

References

Probe Risk Filter — tool.io

Similar or alternative tools

Probe Pvalue Filter
Exclude methylation probes failing a detection p-value threshold.
Blacklist Overlap Filter
Exclude genomic intervals that overlap caller-supplied blacklist intervals.