Up: Component summary
Up: Component summary
Component
CNACaller
Calls significant copy number alterations from a group of segmented copy number
alteration profiles. This component implements the gaia algorithm
for copy number alteration significance estimation. The segments
input can be any segmented copy number sample set, and in Anduril this is
the output of ACGHsegment component.
| Version | 1.0 |
|---|---|
| Bundle | microarray |
| Categories | Copy Number Analysis |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | gaia (R-bioconductor) |
| Source files | component.xml CNACaller.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| segments | CSV | Mandatory | Segmented copy number data. |
| probeAnnotation | CSV | Mandatory | Probe annotation file with probe name (ID), chromosome, start locus, and end locus. End locus is optional. |
Outputs| Name | Type | Description |
|---|---|---|
| regions | CSV | Called regions. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| ampSymbol | string | "1" | Symbol representing amplification call in segments 'CNA_call' column. |
| annotCols | string | "ProbeName,Chr,start,end" | Comma-separated list of probe annotation input column names. The order is significant with probe name, probe chromosome, probe start and end loci. The end locus can be omitted. |
| delSymbol | string | "-1" | Symbol representing deletion call in segments 'CNA_call' column. |
| pLimit | float | 0.25 | Threshold for corrected p-values for calling an alteration significant. |
| segmentCols | string | "ID,chrom,loc.start,loc.end,num.mark,CNA_call" | Comma-separated list of segments input column names. The order is significant with sample id; alteration region chromosome, start and end locus; number of markers in the region; and the copy number alteration call. |
| useApprox | boolean | true | Enable faster calling by using approximate instead of exact computation of background distribution. Non-approximate calling (ie, false) is extremely slow. |
Test cases| Test case | Parameters▼ | IN segments |
IN probeAnnotation |
OUT regions |
||
|---|---|---|---|---|---|---|
| case1 | properties | segments | probeAnnotation | regions | ||
|
annotCols=ProbeName,Chr,start, |
||||||
| case2 | properties | segments | probeAnnotation | (missing) | ||
|
annotCols=ProbeName,Chr,start, |
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