gtxanalyses: Find GWAS analyses

In tobyjohnson/gtx: Genetics ToolboX

Description

Find GWAS analyses matching specified criteria.

Usage

gtxanalyses(analysis, analysis_not, phenotype_contains,
  description_contains, has_tag, ncase_ge, ncohort_ge, has_cleo = FALSE,
  analysis_fields = c("description", "phenotype", "covariates", "cohort",
  "unit", "ncase", "ncontrol", "ncohort"), tag_is, with_tags = FALSE,
  has_access_only = FALSE, dbc = getOption("gtx.dbConnection", NULL))

Arguments

analysis	Key value(s) for GWAS analysis/es required
analysis_not	Key value(s) for GWAS analysis/es not required
phenotype_contains	String to search for in phenotype metadata
description_contains	String to search for in description metadata
has_tag	Tag key value(s) for GWAS analysis/es required
ncase_ge	Numeric to select number of cases greater-or-equal
ncohort_ge	Numeric to select number in cohort greater-or-equal
has_cleo	Logical, select only analyses with CLEO results
analysis_fields	Names of columns/fields to return
tag_is	Internal use only
with_tags	Internal use only
has_access_only	Deprecated
dbc	Database connection

Details

In the near future, a better high level interface will be provided to find GWAS analyses of interest. The gtxanalyses() and gtxwhat() functions were originally intended as internal functions, to abstract part of the functionality required within the phewas() family of functions. However, in the absence of a better interface, these functions are currently exported for users to use.

Value

A data frame of selected rows and columns from TABLE analyses.

Author(s)

Toby Johnson [e-mail]

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.