taxonomy-methods {mia} | R Documentation |
rowData
.These function work on data present in rowData
and define a way to
represent taxonomic data alongside the features of a
SummarizedExperiment
.
TAXONOMY_RANKS taxonomyRanks(x) ## S4 method for signature 'SummarizedExperiment' taxonomyRanks(x) taxonomyRankEmpty( x, rank = taxonomyRanks(x)[1L], empty.fields = c(NA, "", " ", "\t", "-", "_") ) ## S4 method for signature 'SummarizedExperiment' taxonomyRankEmpty( x, rank = taxonomyRanks(x)[1], empty.fields = c(NA, "", " ", "\t", "-", "_") ) checkTaxonomy(x, ...) ## S4 method for signature 'SummarizedExperiment' checkTaxonomy(x) getTaxonomyLabels(x, ...) ## S4 method for signature 'SummarizedExperiment' getTaxonomyLabels( x, empty.fields = c(NA, "", " ", "\t", "-", "_"), with_rank = FALSE, make_unique = TRUE, resolve_loops = FALSE ) taxonomyTree(x, ...) ## S4 method for signature 'SummarizedExperiment' taxonomyTree(x) addTaxonomyTree(x, ...) ## S4 method for signature 'SummarizedExperiment' addTaxonomyTree(x) mapTaxonomy(x, ...) ## S4 method for signature 'SummarizedExperiment' mapTaxonomy(x, taxa = NULL, from = NULL, to = NULL, use_grepl = FALSE) IdTaxaToDataFrame(from)
x |
a
|
rank |
a single character defining a taxonomic rank. Must be a value of
|
empty.fields |
a |
... |
optional arguments not used currently. |
with_rank |
|
make_unique |
|
resolve_loops |
|
taxa |
a |
from |
|
to |
a scalar |
use_grepl |
|
a character
vector of length 8 containing the taxonomy ranks
recognized. In functions this is used as case insensitive.
taxonomyRanks
returns, which columns of rowData(x)
are regarded
as columns containing taxonomic information.
taxonomyRankEmpty
checks, if a selected rank is empty of information.
checkTaxonomy
checks, if taxonomy information is valid and whether
it contains any problems. This is a soft test, which reports some
diagnostic and might mature into a data validator used upon object
creation.
getTaxonomyLabels
generates a character vector per row consisting of
the lowest taxonomic information possible. If data from different levels,
is to be mixed, the taxonomic level is prepended by default.
taxonomyTree
generates a phylo
tree object from the available
taxonomic information. Internally it uses
toTree
and
resolveLoop
to sanitize
data if needed.
IdTaxaToDataFrame
extracts taxonomic results from results of
IdTaxa
.
Taxonomic information from the IdTaxa
function of DECIPHER
package are returned as a special class. With as(taxa,"DataFrame")
the information can be easily converted to a DataFrame
compatible
with storing the taxonomic information a rowData
. Please note that the
assigned confidence information are returned as metatdata
and can
be accessed using metadata(df)$confidence
.
taxonomyRanks
: a character
vector with all the
taxonomic ranks found in colnames(rowData(x))
taxonomyRankEmpty
: a logical
value
mapTaxonomy
: a list
per element of taxa. Each
element is either a DataFrame
, a character
or NULL
.
If all character
results have the length of one, a single
character
vector is returned.
agglomerateByRank
,
toTree
,
resolveLoop
data(GlobalPatterns) GlobalPatterns taxonomyRanks(GlobalPatterns) checkTaxonomy(GlobalPatterns) table(taxonomyRankEmpty(GlobalPatterns,"Kingdom")) table(taxonomyRankEmpty(GlobalPatterns,"Species")) getTaxonomyLabels(GlobalPatterns[1:20,]) # mapTaxonomy ## returns the unique taxonomic information mapTaxonomy(GlobalPatterns) # returns specific unique taxonomic information mapTaxonomy(GlobalPatterns, taxa = "Escherichia") # returns information on a single output mapTaxonomy(GlobalPatterns, taxa = "Escherichia",to="Family") # adding a rowTree() based on the available taxonomic information. Please # note that any tree already stored in rowTree() will be overwritten. x <- GlobalPatterns x <- addTaxonomyTree(x) x