Retrieve phenotype data or phenotype matrix data from the server.

Source: R/phenotype_get_data.R

If input is phenotype matrix object then phenotypes need te have been added to the phenotype matrix object. Create it using get_phenotype_matrix and add to it using phemat_add_phenotype or phemat_add_phenotypes

get_data(pheno_obj, ...)

# S3 method for phenotype
get_data(pheno_obj, conn = NULL, ...)

# S3 method for phenotype_matrix
get_data(pheno_obj, conn = NULL, ...)

# S3 method for playlist
get_data(pheno_obj, missing_value = NULL, base = NULL, ...)

# S3 method for phenotype_list
get_data(pheno_obj, missing_value = NULL, base = NULL, ...)

# S3 method for default
get_data(pheno_obj, conn, missing_value = NA, base = NULL, ...)

Arguments

pheno_obj

phenotype names, phenotype, phenotype matrix or phenotype playlist structure.

...

additional arguments

conn

platform connection structure, create it using platform_connect

missing_value

The string to substitute for a missing value in the data

base

Optional name of base set

Value

tibble from server

Methods (by class)

  • phenotype: Get phenotype data

  • phenotype_matrix: Get data for phenotypes in phenotype matrix

  • playlist: Get data phenotypes in phenotype playlist

  • phenotype_list: Get data phenotypes in phenotype list

  • default: Get data phenotype/s by phenotype names

Examples

if (FALSE) {
api_key <- Sys.getenv("GOR_API_KEY")
project <- Sys.getenv("GOR_PROJECT")
conn <- platform_connect(api_key, project)
phenotype_mat <- get_phenotype_matrix()
phenotype_mat <-  phemat_add_phenotypes(...)
phenotype_data <- get_data(phenotype_mat, conn)
}