Merge pair of phyloseq component data objects of the same class.
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.
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)
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 |
y |
Any |
The merge_phyloseq function is recommended in general.
Special note: non-identical trees are merged using consensus.
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.
#
## # 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))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.