Description Usage Arguments Details Value See Also
View source: R/taxdumpChangeParent.R
Change a node's parent in the NCBI taxonomy.
1 | taxdumpChangeParent(x, taxon, new.parent, orphaned.parent = "synonym")
|
x |
An object of class |
taxon |
A character string giving the name of the taxon. |
new.parent |
A character string giving the name of the new parent taxon. |
orphaned.parent |
A character string indicating how to treat previous
parent taxa, that do not have other children than |
Two choices are possible for orphaned.parent
: (1)
"synonym"
will classify the previous, orphaned parent as a synonym
of "new.parent"
, whereas (2) "delete"
will simply delete the
orphaned parent from the taxonomy.
A data.frame
in parent-child-format, if class(x) ==
"data.frame"
, or TRUE
, if class(x) == "megapteraProj"
. In
the latter case taxdumpChangeParent
is called for its side effect on
the taxonomy table of the database.
ncbiTaxonomy
for downloading the NCBI taxonomy and
dbReadTaxonomy
for reading the project taxonomy; other
taxdump-related tools: taxdumpChildren
,
taxdumpDropTip
, taxdumpHigherRank
,
taxdumpMRCA
, taxdumpSubset
,
taxdump2phylo
and taxdump_isTerminal
.
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