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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)
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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,
useApprox=true

case2 properties segments probeAnnotation (missing)

annotCols=ProbeName,Chr,start,
useApprox=true,
ampSymbol=-1,
delSymbol=1,
pLimit=1,
segmentCols=ID,chr,start,end,nummark,CNAcall


Generated 2018-12-11 07:42:06 by Anduril 2.0.0