RAM (version 1.2.0)

core.Taxa: Show Summary of Core Taxa

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 to be analyzed.

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.

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)
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)