copy_number_loh
Read-only
Recompute loss of heterozygosity from an Affymetrix array's own per-marker genotype calls, rather than reading the runs the producer wrote: APT's window method, with the false-positive rate and the assumed genotyping error rate as parameters. Answers where a sample has lost one parental haplotype, including where copy number is normal. Needs a container that states genotype calls — an OncoScan OSCHP does; a CytoScan CYCHP states the set with no rows, and this says so rather than answering empty.
Input Schema
TableJSON 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 are several. | |
| alpha | No | APT's `lohCN_alpha`: the false-positive rate the heterozygote cutoff is set against. Raising it makes the window narrower and the method readier to call a run, which is the knob to move when comparing against another caller. | |
| _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. | |
| error_rate | No | APT's `lohCN_errorrate`: the assumed genotyping error rate, which is what makes a heterozygote inside a homozygous stretch explicable. It is RE-ESTIMATED from the sample's own no-call rate when the genotype confidences reach the no-call threshold, and the output says which value was actually used. | |
| min_genomic_span | No | APT's `lohCN_minGenomicSpan`: a called run narrower than this many base pairs is dropped. The default is the vendor's 1,000,000. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| runs | Yes | one entry per called run: chromosome (the file's own label), start, end, markers (how many genotyped markers it spans). Coordinates are the marker positions the container states, on whatever assembly it names | |
| window | Yes | what the parameters solved to for THIS sample: markerCount (the window width), hetCutoff (heterozygotes at or above which the window is not LOH), and errorRate (the value used, which differs from the parameter when it was re-estimated from the no-call rate) | |
| summary | Yes | how many runs of loss of heterozygosity were called, over how many chromosomes and how many megabases, and how many markers the method could read | |
| accounting | Yes | markers (genotype calls read), noCalls (dropped before anything else), evaluated, inSegmentsTooShort (markers in a stretch shorter than the window, left UNCALLED rather than called clear), beyondLastChromosome, segments. The five ways a marker can be spent sum to markers | |
| provenance | Yes | which data set the genotype calls came from, which one the coordinates came from, how many were paired, and the parameters in force. The pairing is checked against the marker each call names, never trusted |