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Retrieve data from 1KP

Source: R/retrieve.R
retrieve_onekp.Rd

Download the table of metadata for each transcriptome from the 1KP website (http://www.onekp.com/public_data.html). The metadata are wrapped into a OneKp S4 object. This object contains two data.frames: 1) @table, the main metadata table and 2) @links a map from resource to URL (mostly for internal use).

Usage

retrieve_onekp(add_taxids = TRUE, filter = TRUE)

Arguments

add_taxids

If TRUE, add NCBI taxon ids for each species. This requires downloading the NCBI taxonomy database, which will require a few extra minutes the first time you run the function. This step is necessary only if you wish to filter by NCBI taxon ids.

filter

If TRUE, filter out entries that are associated with a single species (for example crosses or datasets pooled across a genus). If set to TRUE, then add_taxids will also be set to TRUE.

Value

OneKP object

Details

This dataset is also saved as package data, you can access this with data(onekp).

The metadata table contains the following columns:

  • species - species scientific name

  • code - 4-letter 1KP transcriptome unique identifier

  • family - the taxonomic family

  • tissue - the tissue(s) that where sequenced

  • peptides - the filename for the transcript proteins

  • nucleotides - the filename for the transcript DNA

  • tax_id (optional) - the species NCBI taxonomy ID

Examples

if (FALSE) {
# scrape data from the OneKP website 
kp <- retrieve_onekp()
# print to see data summary
kp
# access the metadata table
head(kp@table)
}