copy_number_read
Read-only
Read an Affymetrix copy-number container (CNCHP/CYCHP/OSCHP/CHP) in this project and say what is in it: the algorithm and array that produced it, its data sets and their graphs, the per-chromosome marker index the file carries, and — for one chromosome — each graph decimated to a summary with its real range. Values the analysis left undefined are counted and reported, never plotted as zero. NO GENOME BUILD IS ASSUMED: positions are the file's own, because these files name an annotation release and not an assembly.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| end | No | last base of the region to summarize. Unset is the chromosome's last marker. Given with `start`, the graphs are decimated over that window instead of the whole chromosome: the same thing the panel's Region field does. | |
| bins | No | how many buckets to decimate each graph into. The panel uses one per pixel column of its plot; a smaller number here is a coarser summary of the same data. | |
| 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. | |
| start | No | first base of the region to summarize, on the selected chromosome. Unset is the chromosome's first marker. Clamped to what the file's markers actually cover, because a locus is a position in the assembly and an array's coverage stops where it stops. | |
| _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 | No | a SECOND copy-number file in this project, by name, to read over the SAME chromosome, the same window and the same buckets — the overlay the canvas draws, as numbers. Its chromosome is matched by LABEL and not by number, because each file states its own numbering, and its graphs are matched by COLUMN NAME, so a file carrying a different set of them reports which it has rather than answering from whatever sits at that position. Unset, nothing of a second file is read. | |
| _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's markers to summarize, as THE FILE numbers them. The autosomes are 1-22; which numbers are X and Y is stated by the file's own header (`xChromosome`/`yChromosome`, which both bundled arrays give as 24 and 25) and read from it rather than assumed. Unset is the first the index carries, which is what the panel selects. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| lanes | Yes | the tracks above drawn as the canvas draws them: one lane per graph over the same window, the bucket min-max envelope with its mean over it, the compared sample's envelope behind it where `compare` named a second file, and the marker lane underneath, because a gap in the probes is not a deletion. Null when no graph was decimated — no chromosome was selected, or none of its markers carried a value | |
| tracks | Yes | the selected chromosome decimated: per graph, its fitted range, the bucket minima/maxima/means, and how many markers carried no value | |
| summary | Yes | the file in one sentence, generated from this run — the panel's own facts | |
| compared | Yes | null unless `compare` named a second file. Otherwise: file, dataSet, chromosomeLabel and chromosomeInThatFile (matched by LABEL, so the number may differ), markersOnChromosome and markersInWindow (ITS markers — a different array covers a chromosome at a different density), bins and binnedOver (the SAME buckets and the same extent as `tracks`, which is what makes the two comparable at a coordinate), and tracks: one entry per graph of the PRIMARY file, each with that graph's buckets in the compared sample, or `absent` naming the column the compared file does not carry. A `refused` field instead of the rest means the comparison could not be made and says why — never an empty list, which would read as the two samples agreeing | |
| data_sets | Yes | every data set, with its row count, its columns and which of them are graphs | |
| provenance | Yes | the header chain the file states about itself: algorithm, version, array, and the annotation release it was analyzed against | |
| chromosomes | Yes | the file's OWN per-chromosome index — start row, marker count and display flag each. This is what makes a chromosome one ranged read rather than a whole-file scan. A CNCHP states it in the data set's parameters and a CYCHP as rows in Chromosomes/Summary; both are read, and `index_source` says which one answered | |
| index_source | Yes | where the per-chromosome index above came from, because the two container shapes keep it in different places and a reader comparing two files should not have to guess which |