core.Taxa: Show Summary of Core Taxa

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function returns a list showing taxa at the given taxonomic rank that present in a pre-defined percent of samples in each level of a given metadata category.

Usage

core.Taxa(data, is.OTU=FALSE, rank="g",
         drop.unclassified=TRUE,
         meta, meta.factor="", percent=1)

Arguments

data	a list of OTU tables or taxonomy abundance matrices.
is.OTU	logical. If TRUE, data is an OTU table; otherwise a taxonomy abundance matrix should be provided.
rank	the taxonomic rank of classification (see ?RAM.rank.formatting for formatting details).
drop.unclassified	logical, whether or not exclude unclassified groups. See also tax.abund
meta	the metadata table to be analyzed.
meta.factor	the metadata qualitative variable
percent	the percent of samples in each level of the given metadata variable

Value

core.Taxa returns a list containing taxa at a given rank that present in a pre-defined percent of samples in each level of a given metadata category. The outputs describe the following information for each level of a given metadata variable: 1) core taxa; 2) percent of core taxa sequences vs. total sequences in each levels of the given metadata variable. The last item in the list show the same information of taxa that in all levels.

Note

The taxa are determined to be absent/present using the "pa" method from the function decostand.

Author(s)

Wen Chen

See Also

decostand

Examples

data(ITS1, meta)
# taxa shared by 50 percent samples of each city
core <- core.Taxa(data=list(ITS1=ITS1), is.OTU=TRUE, meta=meta,
                  rank="g", meta.factor="City", percent=0.5)
## Not run: 
data(ITS1, ITS2, meta)
core <- core.Taxa(data=list(ITS1=ITS1, ITS2=ITS2), is.OTU=TRUE,
                  meta=meta, rank="g", meta.factor="City",
                  percent=0.7)
# use taxonomy abundance matrix
g1<-tax.abund(ITS1, rank="g")
core <- core.Taxa(data=list(genus_ITS1=g1), is.OTU=FALSE, 
                  meta=meta, rank="g", meta.factor="City", 
                  percent=0.9)

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-3
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Warning message:
In core.Taxa(data = list(genus_ITS1 = g1), is.OTU = FALSE, meta = meta,  :
  data are not otu tables, will ignore the rank provided

RAM documentation built on May 2, 2019, 3:04 p.m.