merge_phyloseq: Merge arguments into one phyloseq object.

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

Merge arguments into one phyloseq object.

Description

Takes a comma-separated list of phyloseq objects as arguments, and returns the most-comprehensive single phyloseq object possible.

Usage

merge_phyloseq(...)

Arguments

...	a comma-separated list of phyloseq objects.

Details

Higher-order objects can be created if arguments are appropriate component data types of different classes, and this should mirror the behavior of the phyloseq method, which is the suggested method if the goal is simply to create a higher-order phyloseq object from different data types (1 of each class) describing the same experiment.

By contrast, this method is intended for situations in which one wants to combine multiple higher-order objects, or multiple core component data objects (e.g. more than one otu_table) that should be combined into one object.

Merges are performed by first separating higher-order objects into a list of their component objects; then, merging any component objects of the same class into one object according to the behavior desribed in merge_phyloseq_pair; and finally, building back up a merged-object according to the constructor behavior of the phyloseq method. If the arguments contain only a single component type – several otu_table objects, for example – then a single merged object of that component type is returned.

Value

Merges are performed by first separating higher-order objects into a list of their component objects; then, merging any component objects of the same class into one object according to the behavior desribed in merge_phyloseq_pair; and finally, re-building a merged-object according to the constructor behavior of the phyloseq method. If the arguments contain only a single component type – several otu_table objects, for example – then a single merged object of the relevant component type is returned.

Merges between 2 or more tree objects are ultimately done using consensus from the ape package. This has the potential to limit somewhat the final data object, because trees don't merge with other trees in the same granular manner as data tables, and ultimately the species/taxa in higher-order phyloseq objects will be clipped to what is contained in the tree. If this an issue, the tree component should be ommitted from the argument list.

Examples

#
## # Make a random complex object
## OTU1 <- otu_table(matrix(sample(0:5,250,TRUE),25,10), taxa_are_rows=TRUE)
## tax1 <- tax_table(matrix("abc", 30, 8))
## map1 <- data.frame( matrix(sample(0:3,250,TRUE),25,10), 
##   matrix(sample(c("a","b","c"),150,TRUE), 25, 6) ) 
## map1 <- sample_data(map1)
## exam1 <- phyloseq(OTU1, map1, tax1)
## x <- exam1
## x <- phyloseq(exam1)
## y <- tax_table(exam1)
## merge_phyloseq(x, y)
## merge_phyloseq(y, y, y, y)

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.