dynamicThreshold

root

two options either readnum or coverage; coverage is experimental, use readnum

mode

which type of thresholding method to use

thresholding

dynamicThreshold tries to identify the lower bound converage value in order to remove low quality contigs.
Number of contigs tend to stablize at a value when removing reads below a certain readnum and we try to identify the min read required for that region of stability

internal

Functions for path based queries against 'Omics' <https://github.com/etheleon/omics-neo4j-container>, a 'NEO4J' <https://neo4j.com/> database populated with data from metagenomic surveys and their accompanying metabolic and taxonomic annotations.

Wesley GOI

MetamapsDB

Network Analysis of Metabolic Pathways and Gene Based Assemblies
in Metagenomics

dynamicThreshold function

dynamicThreshold tries to identify the lower bound converage value in order to remove low quality contigs.
Number of contigs tend to stablize at a value when removing reads below a certain readnum and we try to identify the min read required for that region of stability — dynamicThreshold

dynamicThreshold tries to identify the lower bound converage value in order to remove low quality contigs.
Number of contigs tend to stablize at a value when removing reads below a certain readnum and we try to identify the min read required for that region of stability

dynamicThreshold: dynamicThreshold tries to identify the lower bound converage value in order to remove low quality contigs. Number of contigs tend to stablize at a value when removing reads below a certain readnum and we try to identify the min read required for that region of stability

Description

Usage

Arguments