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RegionReport

Generates statistics about the DNA regions. The statistics include a length distribution and the frequencies of regions for each chromosome.

Version 1.1
Bundle microarray
Categories Latex Short-read Sequencing
Authors Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Requires R
Source files component.xml RegionReport.r
Usage Example with default values

Inputs

Name Type Mandatory Description
regions CSV Mandatory List of genome regions
chromosomes CSV Optional Table of chromosomes (row names) and their lengths in base pairs

Outputs

Name Type Description
report Latex Statistics report

Parameters

Name Type Default Description
chrColumn string "chr" Name of the chromosome column in input
endColumn string "end" Name of the start locus column in input
lengthColumn string "length" Name of the length column in chromosomes input
sectionType string "subsection" Latex definition for the section level
startColumn string "start" Name of the start locus column in input
title string "DNA region" Name of the DNA region set

Test cases

Test case Parameters IN
regions
IN
chromosomes
OUT
report
case1 (missing) regions (missing) report
case2 properties regions chromosomes report

title = DNA region report,
chrColumn = Chr,
startColumn = Start,
endColumn = End,
lengthColumn = Length,
sectionType = section

case3_empty properties regions (missing) report

title = An empty file


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