copy_number_compare
Read-only
Join two Affymetrix copy-number samples' own calls and report which events they share and which only one of them carries: for every pair, the chromosome both files resolved to, the kind, the bases they overlap and their reciprocal overlap; and separately each sample's unshared calls.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| file | No | which copy-number file in this project is the first sample, by name. Unset, it is the project's only one — and it refuses rather than guessing when there is more than one. | |
| _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. | |
| compare | Yes | which copy-number file in this project is the second sample, by name — the same parameter copy_number_read.compare takes. Required: there is no default second sample, and a file compared with itself answers one question twice. | |
| _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 of the first file to scan, by name. Unset is the file's FIRST, which is what the panel opens on. | |
| min_bases | No | ignore any call spanning fewer bases than this, on BOTH sides. Default 0, for the same reason as min_markers. Note a single-marker call spans 0 bases. | |
| min_markers | No | ignore any call shorter than this many markers, on BOTH sides. The default counts everything either file called, because a reporting floor belongs to the laboratory and not to this tool — and it is the same floor copy_number_findings applies. | |
| compare_data_set | No | which data set of the second file to scan. Unset is that file's FIRST. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| shared | Yes | one entry per PAIR of overlapping calls of the same kind: chrom (the name BOTH files resolved to, never either file's raw chromosome number), kind, a and b (the two calls, each with its own start, end, marker count and value), overlapBases, and reciprocalOverlap — the SMALLER of the two containment fractions, so a focal call inside a whole-arm one scores low rather than 100%. A call that overlaps several on the other side appears once per pair, which is how the reference application's own overlap table behaves | |
| summary | Yes | how many of each sample's own calls are shared and in how many overlapping pairs (a call can overlap several on the other side, so the two differ), how many each carries alone, over how many chromosomes both files index, and which floors were applied | |
| compared | Yes | the chromosome names both files index — what this comparison actually covers, so a caller can tell a clean result from a narrow one | |
| provenance | Yes | which two files and data sets answered, how each side’s calls were read (the producer’s own segment calls, or the per-marker state columns), how many calls each side contributed, and the floors applied to both | |
| only_in_file | Yes | the first sample’s calls that no call of the same kind in the second sample overlaps, on a chromosome BOTH files index — each with the chromosome name and the call itself. This is the half a reader cannot get by reading two result sets one after the other | |
| only_in_compare | Yes | the second sample’s calls that no call of the same kind in the first sample overlaps, on a chromosome both files index | |
| unmatched_chromosomes | Yes | chromosomes only one of the two files indexes, each with which side carries it. Their calls were NOT compared and are NOT in only_in_file or only_in_compare: a targeted array that does not carry Y says nothing about Y in the other sample |