alphadat: Alpha diversity data.
In metamicrobiomeR: Microbiome Data Analysis & Meta-Analysis with GAMLSS-BEZI & Random Effects
Description
Usage
Format
Source
References
Examples
Description
Alpha diversity data from alpha_rarefaction output from QIIME.
Usage
1
Format
A list of 4 dataframes for four indexes: Chao1, Observed_species, PD_whole_tree, Shannon.
Source
References
Subramanian et al. Nature. 2014 Jun 19; 510(7505): 417–421.
(PubMed)
Examples
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data(alphadat)
# Load covariate data
data(covar.rm)
covar.rm$sampleid<-tolower(covar.rm$sampleid)
#comparison of standardized alpha diversity indexes between genders adjusting for
#breastfeeding and infant age at sample collection in infants <=6 months of age
alphacom<-alpha.compare(datlist=alphadat,depth=3,mapfile=covar.rm,
mapsampleid="sampleid", comvar="gender",adjustvar=c("age.sample","bf"),
longitudinal="yes", age.limit=6,standardize=TRUE)
alphacom$alphasum[,1:5]
metamicrobiomeR documentation built on Nov. 9, 2020, 5:06 p.m.
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Description Usage Format Source References Examples
Description
Alpha diversity data from alpha_rarefaction output from QIIME.
Usage
1 |
Format
A list of 4 dataframes for four indexes: Chao1, Observed_species, PD_whole_tree, Shannon.
Source
References
Subramanian et al. Nature. 2014 Jun 19; 510(7505): 417–421. (PubMed)
Examples
1 2 3 4 5 6 7 8 9 10 | data(alphadat)
# Load covariate data
data(covar.rm)
covar.rm$sampleid<-tolower(covar.rm$sampleid)
#comparison of standardized alpha diversity indexes between genders adjusting for
#breastfeeding and infant age at sample collection in infants <=6 months of age
alphacom<-alpha.compare(datlist=alphadat,depth=3,mapfile=covar.rm,
mapsampleid="sampleid", comvar="gender",adjustvar=c("age.sample","bf"),
longitudinal="yes", age.limit=6,standardize=TRUE)
alphacom$alphasum[,1:5]
|
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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