core_matrix: Core Matrix
In microbiome: Microbiome Analytics
Description
Usage
Arguments
Value
Author(s)
References
Examples
Description
Creates the core matrix.
Usage
1
core_matrix(x, prevalences = seq(0.1, 1, , 1), detections = NULL)
Arguments
x
phyloseq object or a taxa x samples abundance matrix
prevalences
a vector of prevalence percentages in [0,1]
detections
a vector of intensities around the data range
Value
Estimated core microbiota
Author(s)
Contact: Jarkko Salojarvi microbiome-admin@googlegroups.com
References
A Salonen et al. The adult intestinal core microbiota is determined by
analysis depth and health status. Clinical Microbiology and Infection
18(S4):16 20, 2012.
To cite the microbiome R package, see citation('microbiome')
Examples
1
2
3
# Not exported
#data(peerj32)
#core <- core_matrix(peerj32$phyloseq)
microbiome documentation built on Nov. 8, 2020, 5:08 p.m.
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Description Usage Arguments Value Author(s) References Examples
Description
Creates the core matrix.
Usage
1 | core_matrix(x, prevalences = seq(0.1, 1, , 1), detections = NULL)
|
Arguments
x |
|
prevalences |
a vector of prevalence percentages in [0,1] |
detections |
a vector of intensities around the data range |
Value
Estimated core microbiota
Author(s)
Contact: Jarkko Salojarvi microbiome-admin@googlegroups.com
References
A Salonen et al. The adult intestinal core microbiota is determined by analysis depth and health status. Clinical Microbiology and Infection 18(S4):16 20, 2012. To cite the microbiome R package, see citation('microbiome')
Examples
1 2 3 | # Not exported
#data(peerj32)
#core <- core_matrix(peerj32$phyloseq)
|
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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