Description Usage Arguments Details Value Author(s) See Also Examples
For an object of class biom
,
find row or column annotations (BIOM metadata
)
that match by name a given pattern,
or append new annotations.
1 2 3 4 5 |
x |
an object ( |
pattern |
literal string or regular expression identifying metadata by name ( |
name |
name for new metadata annotation ( |
value |
new metadata, one value per row/column |
Complete technical documentation is forthcoming. For the current preliminary release, please refer to the examples provided.
For rows()
and columns()
,
a data.frame
consisting of the metadata of x
matching pattern
by name.
For the replacement functions,
the object x
with updated metadata.
Daniel T. Braithwaite
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | #### exact sampling locations returned in a data.frame
columns (xx3, "latitude|longitude")
#### a data.frame is returned even in case of a single matching metadata field
is.data.frame (columns (xx1, "sample.data.biome"))
#### project IDs and environmental package metadata -- note regex here and above
colnames (columns (xx2, "project\\.id|^env_package"))
#### row metadata makes annotation hierarchy levels available,
#### so typical row metadata has few components, and here just two
names (rows (xx1))
rows (xx1, "ontology1")
#### here, the rownames and the (single) variable of the data.frame coincide
rows (xx1, "ontology2")
#### variables are almost always coded as factors
is.factor (columns (xx1, "sample.data.biome") [[1]])
|
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