# ncbi_taxon_sample

From metacoder v0.1.2
by Zachary Foster

##### Download representative sequences for a taxon

Downloads a sample of sequences meant to evenly capture the diversity of a given taxon.
Can be used to get a shallow sampling of a vast groups.
**CAUTION:** This function can make MANY queries to Genbank depending on arguments given and
can take a very long time.
Choose your arguments carefully to avoid long waits and needlessly stressing NCBI's servers.
Use a downloaded database and `extract_taxonomy`

when possible.

- Keywords
- internal

##### Usage

`ncbi_taxon_sample(name = NULL, id = NULL, target_rank, min_counts = NULL, max_counts = NULL, interpolate_min = TRUE, interpolate_max = TRUE, min_length = 1, max_length = 10000, min_children = NULL, max_children = NULL, verbose = TRUE, ...)`

##### Arguments

- name
- (
`character`

of length 1) The taxon to download a sample of sequences for. - id
- (
`character`

of length 1) The taxon id to download a sample of sequences for. - target_rank
- (
`character`

of length 1) The finest taxonomic rank at which to sample. The finest rank at which replication occurs. Must be a finer rank than`taxon`

. Use`get_taxonomy_levels`

to see available ranks. - min_counts
- (named
`numeric`

) The minimum number of sequences to download for each taxonomic rank. The names correspond to taxonomic ranks. - max_counts
- (named
`numeric`

) The maximum number of sequences to download for each taxonomic rank. The names correspond to taxonomic ranks. - interpolate_min
- (
`logical`

) If`TRUE`

, values supplied to`min_counts`

and`min_children`

will be used to infer the values of intermediate ranks not specified. Linear interpolation between values of spcified ranks will be used to determine values of unspecified ranks. - interpolate_max
- (
`logical`

) If`TRUE`

, values supplied to`max_counts`

and`max_children`

will be used to infer the values of intermediate ranks not specified. Linear interpolation between values of spcified ranks will be used to determine values of unspecified ranks. - min_length
- (
`numeric`

of length 1) The minimum length of sequences that will be returned. - max_length
- (
`numeric`

of length 1) The maximum length of sequences that will be returned. - min_children
- (named
`numeric`

) The minimum number sub-taxa of taxa for a given rank must have for its sequences to be searched. The names correspond to taxonomic ranks. - max_children
- (named
`numeric`

) The maximum number sub-taxa of taxa for a given rank must have for its sequences to be searched. The names correspond to taxonomic ranks. - verbose
- (
`logical`

) If`TRUE`

, progress messages will be printed. - ...
- Additional arguments are passed to
`ncbi_searcher`

.

##### Details

See `get_taxonomy_levels`

for available taxonomic ranks.

##### Examples

```
## Not run:
# ncbi_taxon_sample(name = "oomycetes", target_rank = "genus")
# data <- ncbi_taxon_sample(name = "fungi", target_rank = "phylum",
# max_counts = c(phylum = 30),
# entrez_query = "18S[All Fields] AND 28S[All Fields]",
# min_length = 600, max_length = 10000)
# ## End(Not run)
```

*Documentation reproduced from package metacoder, version 0.1.2, License: GPL-2 | GPL-3*

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