README.md

In tparkerd/deathly-parsley: GWAS Database Connection R Package for Plants

Plant Genome-wide Association Study Database Connector (PGWASDBC)

Installation

Use devtools or remotes to install the package from GitHub. Below is an example of how to install the package using devtools.

devtools::install_github("danforthcenter/pgwasdbc")

Usage

To query the database from your code, you can use the namespace pgwasdbc.

Below is a list of the functions available.

list_bp_by_liketrait_for_species(trait, species, cutoff)

List of SNP number, chromosome, trait, for a species given a p-value cutoff

Arguments

trait (string) - name of the trait (case insensitive), the name can be a substring of the desired trait
species (string) - binomial name of species (e.g., "Zea mays")
cutoff (numeric) - maximum p-value cutoff, inclusive

list_bp_by_trait_for_species(trait, species, cutoff)`

List of SNP number, chromosome, trait, for a species given a p-value cutoff

Arguments

trait (string) - name of the trait (case insensitive)
species (string) - binomial name of species (e.g., "Zea mays")
cutoff (numeric) - maximum p-value cutoff, inclusive

list_traits()

List name of all traits

list_species()

Lists binomial name and shortname for all species

list_growouts()

Lists growout name and location code for all growouts

list_traits_for_species(species)

Lists all known traits for a given species (by binomial name)

Arguemnts

species (string) - binomial name of species

query(sql)

Execute a SQL statement; allows to running custom queries against the database. Permitted actions are limited by granted permissions on database for assigned user.

Arguments

sql (string) - SQL statement (e.g., "SELECT * FROM species")

Example of pulling trait data using predefined queries

pgwasdbc::list_bp_by_liketrait_for_species(trait = "As75", cutoff = 0.01, species = "Zea mays")

Example user-defined query

pgwasdbc::query("SELECT * from trait")

Troubleshooting

Since this package depends on PostgreSQL drivers, you may need to manually install your operating system's respective Postgres development drivers.

Debian, Ubuntu

sudo apt install libpq-dev

Additional Information

Google Doc: Implementation & Feature Requests

tparkerd/deathly-parsley documentation built on Nov. 5, 2019, 10:56 a.m.