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PeakScore

Calculates a cumulative score for each gene having some regions assigned to it. The score is based on the distance of the region. The closer or the more assigned regions a gene has the better score it will obtain.

For each gene (g) assignment (p) with an optional score (w) the output score_p is w*(s-distance)/s or w*(e^(-distance/s)) depending on the selected formula (linear or exponential). The cumulative score is incremented if score_p > 0: score_g=score_g+score_p.

Version 1.2
Bundle microarray
Categories Annotation Short-read Sequencing
Authors Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Requires microarray.jar (jar)
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
in CSV Mandatory Distances of the genes

Outputs

Name Type Description
out AnnotationTable Table that contains the gene IDs and the corresponding scores

Parameters

Name Type Default Description
distColumn string (no default) Name of the distance column in input
formula string "linear" Selection of the score function (exponential or linear)
idColumn string (no default) Name of the identifier column in input
minScore float 1.0 Genes must obtain at least this score to be listed in output.
peaksColOut string "peaks" Name of the output column, which contains the peak counts
s float 100000 Scaling term for the distances that is the maximum distance
scoreColOut string "score" Name of the output column, which contains the gene scores
scoreColumn string "" Column name for the peak scores or an empty string for constant one

Test cases

Test case Parameters IN
in
OUT
out
case1 properties in out

distColumn = distance,
idColumn = .GeneId,
minScore = 0.0,
scoreColOut = foo,
peaksColOut = bar

case2 properties in out

scoreColumn = score,
distColumn = distance,
idColumn = .GeneId,
minScore = 1.0

case3 properties in out

formula = exponential,
distColumn = distance,
idColumn = .GeneId,
minScore = 0.0


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