simulateData: OTU counts simulation
In MiSPU: Microbiome Based Sum of Powered Score (MiSPU) Tests
Description
Usage
Arguments
Value
Author(s)
References
Examples
Description
We used a phylogenetic tree of OTUs from a real throat microbiome data set, which consists of 856 OTUs after discarding singleton OTUs. Then based on a complicate statistical meodel, we generated the OTU counts for each individual to simulate the feature of real microbiome data.
Usage
1
simulateData(nSam=100, s=12, ncluster = 20, mu = 1000, size = 25)
Arguments
nSam
Sample size, the default value is 100.
s
The indicator of informative cluster.
ncluster
Positive integer specifying the number of clusters of they phylogenetic tree.
mu
The mean of the negative binomial distribution.
size
The size of the negative binomial distribution
Value
A list object, including the informative OTU counts table and whole OTU counts table.
Author(s)
Chong Wu
References
Chong, W., Pan, W. (2015) An Adaptive Association Test for Microbiome Data, submitted.
Examples
1
2
OTU = simulateData()
OTU
Example output
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: ape
Loading required package: aSPU
Loading required package: gee
Loading required package: MASS
Loading required package: mvtnorm
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-1 (2017-07-02) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: maps
Loading required package: matrixStats
Loading required package: cluster
Attaching package: 'cluster'
The following object is masked from 'package:maps':
votes.repub
$informative.OTU
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MiSPU documentation built on May 1, 2019, 8:41 p.m.
R Package Documentation
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Description Usage Arguments Value Author(s) References Examples
Description
We used a phylogenetic tree of OTUs from a real throat microbiome data set, which consists of 856 OTUs after discarding singleton OTUs. Then based on a complicate statistical meodel, we generated the OTU counts for each individual to simulate the feature of real microbiome data.
Usage
1 | simulateData(nSam=100, s=12, ncluster = 20, mu = 1000, size = 25)
|
Arguments
nSam |
Sample size, the default value is 100. |
s |
The indicator of informative cluster. |
ncluster |
Positive integer specifying the number of clusters of they phylogenetic tree. |
mu |
The mean of the negative binomial distribution. |
size |
The size of the negative binomial distribution |
Value
A list object, including the informative OTU counts table and whole OTU counts table.
Author(s)
Chong Wu
References
Chong, W., Pan, W. (2015) An Adaptive Association Test for Microbiome Data, submitted.
Examples
1 2 | OTU = simulateData()
OTU
|
Example output
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: ape
Loading required package: aSPU
Loading required package: gee
Loading required package: MASS
Loading required package: mvtnorm
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-1 (2017-07-02) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: maps
Loading required package: matrixStats
Loading required package: cluster
Attaching package: 'cluster'
The following object is masked from 'package:maps':
votes.repub
$informative.OTU
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