Description
Usage
Arguments
Details
Examples
View source: R/sequence_download.R
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.
 ( = , id = , target_rank, min_counts = ,
max_counts = , interpolate_min = , interpolate_max = ,
min_length = 1, max_length = 10000, min_children = ,
max_children = , verbose = , )

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 subtaxa 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 subtaxa 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 .

See get_taxonomy_levels
for available taxonomic ranks.
 ## Not run:
( = "oomycetes", target_rank = "genus")
< ( = "fungi", target_rank = "phylum",
max_counts = (phylum = 30),
entrez_query = "18S[All Fields] AND 28S[All Fields]",
min_length = 600, max_length = 10000)
## End(Not run)

metacoder documentation built on May 30, 2017, 3:11 a.m.