copy_number_mosaicism
Estimate which mosaic fraction class each region of one chromosome is closest to, as Affymetrix Power Tools computes it. A mosaic event is present in only some of the sample's cells, so its log2 ratio sits between the levels a clonal change would produce. Every segment comes back with the class it was assigned (±0.3, ±0.5, ±0.7, ±1.0), the fraction that class is NAMED for, its confidence, and whether the method CALLED it as mosaic — a whole-copy change of exactly ±1.0 is clonal and is reported with call 0, which is the vendor's own test. The mixture values are class labels, not measured cell fractions: there is no published method for this estimate and no independent implementation to grade it against, so it is reported as APT computes it and the provenance output carries that sentence. A chromosome with fewer than 4,330 markers is refused by name rather than answered empty, because the method's own boundary adjustments would delete every call.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| file | No | which copy-number file in this project, by name. Unset, it is the project's only one — and it refuses rather than guessing when there is more than one. | |
| graph | No | which graph column to read. Unset is the first log2-ratio column, the same rule copy_number_segment applies. A column that is not a log2 ratio is refused rather than smoothed: a copy-number STATE column is already someone's answer. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| data_set | No | which data set to read, by name. Unset is the file's FIRST, which is what the panel opens on. | |
| chromosome | No | which chromosome, as the file numbers them (1-22, then 23=X, 24=Y, 25=MT — the file's own convention). Unset is the first the index carries. A chromosome too short for the method is refused with the count it has and the ones that would run. | |
| mosaic_bandwidth | No | the smoothing window in markers — APT's own `marker-bandwidth`. A mosaic event is a shallow wide elevation, so this is what decides how wide 'wide' is. The default is the vendor's shipped value. | |
| mosaic_confidence_window | No | the running-median window used to score a segment, in markers — APT's own `confidence-window`. The default is the vendor's shipped value. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| called | Yes | the subset of segments with call === 1 — the mosaic events themselves, separated out so a pipeline does not have to know the vendor’s clonal test to find them | |
| summary | Yes | how many segments the method produced, how many of them it CALLED as mosaic, which classes they fall in, and which chromosome and column answered | |
| segments | Yes | every segment: startPosition and endPosition in bases, startIndex and endIndex in markers, mixture (the class as APT numbers it), mixtureValue (the fraction that class is NAMED for — a label, not a measurement), confidence, and call, which is 1 only for a segment the method calls mosaic. A reader looking for mosaic events wants call === 1 | |
| provenance | Yes | which file, data set, chromosome and column answered, how many markers were read, the windows and the eight class boundaries the run used, and the sentence this estimate must be presented with — verbatim from the engine, never paraphrased |