list_prevalent_groups: List prevalent groups
In microbiome/microbiomeold: Tools for microbiome analysis
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
List prevalent groups
Usage
1
list_prevalent_groups(x, detection.threshold, prevalence.threshold)
Arguments
x
Abundance data matrix: samples x features (microbes)
detection.threshold
Detection threshold for absence/presence.
prevalence.threshold
Detection threshold for prevalence
Details
Lists groups that are more prevalent above the detection
threshold as specified by the detection and prevalence threshold
arguments
Value
Vector of prevalent groups
Author(s)
Contact: Leo Lahti 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
data(peerj32)
list_prevalent_groups(peerj32$microbes, 2, 0.2)
microbiome/microbiomeold documentation built on May 22, 2019, 9:57 p.m.
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Description Usage Arguments Details Value Author(s) References Examples
Description
List prevalent groups
Usage
1 | list_prevalent_groups(x, detection.threshold, prevalence.threshold)
|
Arguments
x |
Abundance data matrix: samples x features (microbes) |
detection.threshold |
Detection threshold for absence/presence. |
prevalence.threshold |
Detection threshold for prevalence |
Details
Lists groups that are more prevalent above the detection threshold as specified by the detection and prevalence threshold arguments
Value
Vector of prevalent groups
Author(s)
Contact: Leo Lahti microbiome-admin@googlegroups.com
References
A Salonen et al. The adult intestinal core microbiota is determined by analysis depth and health status. Clinical Microbiology and Infection 18(S4):16 20, 2012. To cite the microbiome R package, see citation('microbiome')
Examples
1 2 | data(peerj32)
list_prevalent_groups(peerj32$microbes, 2, 0.2)
|
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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