phyloseq -> MicrobiomeExperiment low-level data translation document

[hcorrada]

No description provided.

[joey711]

@joey711 when this is closed good idea to start testing migration in https://github.com/joey711/phyloseq/tree/MicrobiomeExperiment

[hcorrada]

From phyloseq vignette:

Function	Returns
[	Standard extraction operator. Works on otu_table, sample_data, and taxonomyTable
access	General slot accessor function for MicrobiomeExperiment-package
get_taxa	Abundance values of all taxa in sample `i'
get_sample	Abundance values of taxa `i' for all samples
get_taxa_unique	A unique vector of the observed taxa at a particular taxonomic rank
get_variable	An individual sample variable vector/factor
nsamples	Get the number of samples described by an object
ntaxa	Get the number of OTUs (taxa) described by an object
otu_table	Build or access otu_table objects
rank_names	Get the names of the available taxonomic ranks
sample_data	Build or access sample_data objects
sample_names	The names of all samples
taxa_names	The names of all taxa
sample_sums	The sum of the abundance values of each sample
sample_variables	The names of sample variables
taxa_sums	The sum of the abundance values of each taxa
taxa_are_rows	TRUE if taxa are row indices in otu_table
tax_table	A taxonomy table
phy_tree	Access the tree contained in a MicrobiomeExperiment object

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[dombraccia]

SE = SummarizedExperiment package
mgF = metagenomeFeatures package
X = no equivalent fucntion contained in specified package

Function	Returns	SE	mgF
[	Standard extraction operator. Works on otu_table, sample_data, and taxonomyTable	[
access	General slot accessor function for MicrobiomeExperiment-package	X	X
get_taxa	Abundance values of all taxa in sample `i'	X	X
get_sample	Abundance values of taxa `i' for all samples	X	X
get_taxa_unique	A unique vector of the observed taxa at a particular taxonomic rank	X	X
get_variable	An individual sample variable vector/factor	X	X
nsamples	Get the number of samples described by an object	X	X
ntaxa	Get the number of OTUs (taxa) described by an object	X	X
otu_table	Build or access otu_table objects	X	X
rank_names	Get the names of the available taxonomic ranks	X	X
sample_data	Build or access sample_data objects	X	X
sample_names	The names of all samples	X	X
taxa_names	The names of all taxa	X	X
sample_sums	The sum of the abundance values of each sample	X	X
sample_variables	The names of sample variables	X	X
taxa_sums	The sum of the abundance values of each taxa	X	X
taxa_are_rows	TRUE if taxa are row indices in otu_table	X	X
tax_table	A taxonomy table	X	X
phy_tree	Access the tree contained in a MicrobiomeExperiment object	X	X

[dombraccia]

NOTE: the majority of phyloseq functions in this table are simple accessor functions or are derivatives of base R functions.

[hcorrada]

[X] add counts accessor
[ ] add taxTable accessor

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[X] clean up taxa_names to use splitTree from TreeIndex