Up: Component summary Function

NovelExprMatrix

Take output of miRanalyzer (or miRDeep2) and create an expression matrix with the putative novel miRNAs found.

Version 1.0
Bundle sequencing
Categories Expression Novel smallRNA
Specialties generic
Authors Katherine Icay (katherine.icay@helsinki.fi)
Issue tracker View/Report issues
Source files component.xml function.scala
Usage Example with default values

Type parameters (generics)

Inputs

Name Type Mandatory Description
novelArray Array<BinaryFile> Mandatory Output array where putative novel miRNA counts can be retrieved per sample.

Outputs

Name Type Description
csv CSV Expression matrix of putative novel miRNA expression, merged across samples, with separate columns for coordinates (chromosome, start, end position, and strand).
csv_wID CSV Expression matrix of putative novel miRNA expression, merged across samples, with a single column of unique IDs based on coordinates.

Parameters

Name Type Default Description
maxLength int 300 Maximum allowed length of merged sequence regions. e.g. The maximum length of a miRNA precursor.
maxPointDistance int 30 Merge the counts of neighbouring putative novel miRNA regions with this maximum (genomic) distance. Chromosome, start, and end positions are used in the calculations.
method string "miranalyzer" Either "miranalyzer" or "mirdeep2" to distinguish what files and where in the files the putative novel miRNAs are written.
minPercent float 0 Minimum percentage of samples that a putative novel miRNA should have counts in to be included in the expression matrix.

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