sq.curate | R Documentation |
After downloading sequences from genbank, this function
curates sequences based on taxonomic
information. Note that this function provides two summary datasets.
First, the accession numbers.
Second, the taxonomic information for each species in the database.
The taxonomy strictly follows
the gbif taxonomic backbone. The resulting files are saved
to "1.CuratedSequences"
. The
resulting files also have the most recent curated taxonomy
following the gbif (or selected database) taxonomic backbone.
sq.curate(
filterTaxonomicCriteria = NULL,
mergeGeneFiles = NULL,
database = "gbif",
kingdom = NULL,
folder = "0.Sequences",
sqs.object = NULL,
removeOutliers = TRUE,
minSeqs = 5,
threshold = 0.05,
ranks = c("kingdom", "phylum", "class", "order", "family", "genus", "species")
)
filterTaxonomicCriteria |
A single string of terms (delimited using "|") listing all the strings that could be used to identify the species that should be in the dataset (character). |
mergeGeneFiles |
A named list, with each element being a character vector
indicating the names of the files in |
database |
A name of a database with taxonomic information. Although 'gbif' is faster, it only has information for animals and plants. Other databases follow taxize::classification. |
kingdom |
Optional and only used when database='gbif'. Two possible options: "animals" or "plants." |
folder |
The name of the folder where the original sequences are located (character). |
sqs.object |
A list of sequences generated from |
removeOutliers |
Whether |
minSeqs |
minimum number of sequences per locus |
threshold |
Relative to |
ranks |
The taxonomic ranks used to examine the taxonomy of the species
in the |
This function will return an object of class list
with the
following elements. First, the curated sequences with original names.
Second, the curated sequences with species-level names. Third,
the accession numbers table. Fourth, a summary of taxonomic
information for all the species sampled in the files.
## Not run:
sq.retrieve.direct(
clades = c("Felis", "Vulpes", "Phoca"),
species = "Manis_pentadactyla",
genes = c("ADORA3", "CYTB")
)
sq.curate(
filterTaxonomicCriteria = "Felis|Vulpes|Phoca|Manis",
database = "gbif", kingdom = "animals",
folder = "0.Sequences"
)
## End(Not run)
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