dynamicThreshold: dynamicThreshold tries to identify the lower bound converage...
In MetamapsDB: Network Analysis of Metabolic Pathways and Gene Based Assemblies in Metagenomics
Description
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
Usage
1
dynamicThreshold(koi, root)
Arguments
koi
KO of interest
root
folder to find
mode
two options either readnum or coverage; coverage is experimental, use readnum
thresholding
which type of thresholding method to use
MetamapsDB documentation built on May 1, 2019, 9:23 p.m.
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Description
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
Usage
1 | dynamicThreshold(koi, root)
|
Arguments
koi |
KO of interest |
root |
folder to find |
mode |
two options either readnum or coverage; coverage is experimental, use readnum |
thresholding |
which type of thresholding method to use |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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