merge_phyloseq_pair-methods: Merge pair of phyloseq component data objects of the same...

In phyloseq: Handling and analysis of high-throughput microbiome census data

Description

Internal S4 methods to combine pairs of objects of classes specified in the phyloseq package. These objects must be component data of the same type (class). This is mainly an internal method, provided to illustrate how merging is performed by the more general merge_phyloseq function.

Usage

merge_phyloseq_pair(x, y)

## S4 method for signature 'otu_table,otu_table'
merge_phyloseq_pair(x, y)

## S4 method for signature 'taxonomyTable,taxonomyTable'
merge_phyloseq_pair(x, y)

## S4 method for signature 'sample_data,sample_data'
merge_phyloseq_pair(x, y)

## S4 method for signature 'phylo,phylo'
merge_phyloseq_pair(x, y)

## S4 method for signature 'XStringSet,XStringSet'
merge_phyloseq_pair(x, y)

Arguments

x	A character vector of the species in object x that you want to keep – OR alternatively – a logical vector where the kept species are TRUE, and length is equal to the number of species in object x. If species is a named logical, the species retained is based on those names. Make sure they are compatible with the taxa_names of the object you are modifying (x).
y	Any phyloseq object.

Details

The merge_phyloseq function is recommended in general.

Special note: non-identical trees are merged using consensus.

Value

A single component data object that matches x and y arguments. The returned object will contain the union of the species and/or samples of each. If there is redundant information between a pair of arguments of the same class, the values in x are used by default. Abundance values are summed for otu_table objects for those elements that describe the same species and sample in x and y.

See Also

merge_phyloseq merge_taxa

Examples

#
## # merge two simulated otu_table objects.
## x  <- otu_table(matrix(sample(0:5,200,TRUE),20,10), taxa_are_rows=TRUE)
## y  <- otu_table(matrix(sample(0:5,300,TRUE),30,10), taxa_are_rows=FALSE)
## xy <- merge_phyloseq_pair(x, y)
## yx <- merge_phyloseq_pair(y, x)
## # merge two simulated tax_table objects
## x <- tax_table(matrix("abc", 20, 6))
## y <- tax_table(matrix("def", 30, 8))
## xy <- merge_phyloseq_pair(x, y)
## # merge two simulated sample_data objects
## x <- data.frame( matrix(sample(0:3,250,TRUE),25,10), 
##   matrix(sample(c("a","b","c"),150,TRUE),25,6) )
## x <- sample_data(x)
## y <- data.frame( matrix(sample(4:6,200,TRUE),20,10), 
##   matrix(sample(c("d","e","f"),120,TRUE),20,8) )
## y <- sample_data(y)
## merge_phyloseq_pair(x, y)
## data.frame(merge_phyloseq_pair(x, y))
## data.frame(merge_phyloseq_pair(y, x))

Example output

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.