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SegmentPlot

Plots segmented chromosomal data. Any chromosomal regions defined with chromosome, start and end locations can be visualized, but the main purpose of this component is to visualize Array CGH segmentation results.

The input table must contain the following columns: Sample, chromosome, starting basepair, ending basepair. Segment call and score are optional columns. These are used to distinguish between duplications and deletions and to assign confidences or ranks to the calls, respectively.

Version 1.5
Bundle microarray
Categories Latex Copy Number Analysis
Authors Riku Louhimo (Riku.Louhimo@Helsinki.FI), Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Requires R ; limma (R-bioconductor)
Source files component.xml SegmentPlot.r
Usage Example with default values

Inputs

Name Type Mandatory Description
chrSegments CSV Mandatory Chromosomal segments, usually obtained from an Array CGH experiment after segmentation.

Outputs

Name Type Description
plot Latex Chromosomal segments, with the significant regions highlighted if there are any.
SignRegion DNARegion The regions that are above the given threshold parameter value. The output includes a column for the frequency of the result segments.

Parameters

Name Type Default Description
bpEndColumn string "end" The name of the chromosomal end location column in the input file.
bpStartColumn string "start" The name of the chromosomal start location column in the input file.
callColumn string "call" The name of the call column in the input file. All calls are considered to be 1 if this parameter value is empty.
chrColumn string "chr" The name of the chromosomal number column in the input file.
drawSampleIDs boolean false Plot sample ids to the start of each row.
excludeChr string "23,24,X,Y,M" Chromosomes that are not used in the analysis. Defaults to excluding mitochondrial and sex chromosomes.
gainsOrLosses int 0 Determine whether to plot gains alone (1) or losses alone (-1) or both (default).
lineWidth float 3 Line width in output plot
sThold float 0.1 The significance threshold. Please note that this is just the fraction of samples we want the segment to be present in.
sampleColumn string "Sample" The name of the sample name column in the input file.
scoreColumn string "" The name of the score column in the input file. You may leave this parameter empty if the data do not contain such information.
scoreMerge string "max" Defines an R function that is used to summarize the score values of all input calls that are contributing to an output regions.

Test cases

Test case Parameters IN
chrSegments
OUT
plot
OUT
SignRegion
case1 (missing) chrSegments plot SignRegion
case2 properties chrSegments plot SignRegion

gainsOrLosses=1,
sThold=0.2

case3 properties chrSegments plot SignRegion

gainsOrLosses=-1,
sThold=0.15,
scoreColumn=start,
scoreMerge=min,
excludeChr=chr7

case4_InvalidCols properties chrSegments (expecting failure) (expecting failure)

bpEndColumn=endCol,
bpStartColumn=startCol,
callColumn=callCol,
chrColumn=chrCol

case5 properties chrSegments plot SignRegion

bpEndColumn=endCol,
bpStartColumn=startCol,
callColumn=callCol,
chrColumn=chrCol,
sampleColumn=SampleCol,
lineWidth=2,
sThold=0.3

case6 properties chrSegments plot SignRegion

sThold=0.1,
lineWidth=1

case8 properties chrSegments (missing) SignRegion

sThold=0.6,
lineWidth=0.6,
gainsOrLosses=-1


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