sq.retrieve.indirect: Retrieve sequences from genbank based on a dataset of...

In cromanpa94/phruta: Phylogenetic Reconstruction and Time-dating

Retrieve sequences from genbank based on a dataset of accession numbers

Description

Downloads sequences from genbank (nucleotide database) for particular taxa and genes into a folder called "0.Sequences".

Usage

sq.retrieve.indirect(acc.table, download.sqs = FALSE)

Arguments

acc.table	An accession table, ideally generated using acc.table.retrieve. The data.frame must have the Species, Acc, and gene column names.
download.sqs	Logical indicating whether sequences should be downloaded locally or returned as a list.

Value

None

Examples

## Not run: 
acc.table.retrieve(
 clades  = c('Felis', 'Vulpes', 'Phoca'),
 species = 'Manis_pentadactyla' ,
 genes   = c("A2AB","ADORA3","ADRB2","APOB",
            "APP","ATP7","BCHE","BDNF",
            "BMI1","BRCA1","BRCA2","CNR1",
            "COI","CREM","CYTB","DMP1",
            "EDG1","ENAM","FBN1","GHR",
            "IRBP","ND1","ND2","PLCB4",
            "PNOC","RAG1a","RAG1b","RAG2",
            "TTN","TYR1","VWF"),
 speciesLevel=TRUE
)

sq.retrieve.indirect(test)


## End(Not run)

cromanpa94/phruta documentation built on July 7, 2024, 4:58 p.m.