Package 'epigraphdb' reference manual

Title:	Interface Package for the 'EpiGraphDB' Platform
Description:	The interface package to access data from the 'EpiGraphDB' <https://epigraphdb.org> platform. It provides easy access to the 'EpiGraphDB' platform with functions that query the corresponding REST endpoints on the API <https://api.epigraphdb.org> and return the response data in the 'tibble' data frame format.
Authors:	Yi Liu [cre, aut], Valeriia Haberland [aut], Marina Vabistsevits [aut], Tom Gaunt [aut], MRC IEU [cph]
Maintainer:	Yi Liu <[email protected]>
License:	GPL-3
Version:	0.2.3
Built:	2024-09-11 03:37:00 UTC
Source:	https://github.com/MRCIEU/epigraphdb-r

MR evidence on confounding traits between exposure and outcome

Description

GET /confounder

Usage

confounder(
  exposure_trait = NULL,
  outcome_trait = NULL,
  type = c("confounder", "intermediate", "reverse_intermediate", "collider"),
  pval_threshold = 1e-05,
  mode = c("table", "raw")
)
confounder(
  exposure_trait = NULL,
  outcome_trait = NULL,
  type = c("confounder", "intermediate", "reverse_intermediate", "collider"),
  pval_threshold = 1e-05,
  mode = c("table", "raw")
)

Arguments

`exposure_trait`	A trait name, e.g. "Body mass index", leaving `exposure_trait` as `NULL` will return MR information related to a specific `outcome`. NOTE: `exposure_trait` and `outcome_trait` cannot be both `NULL`.
`outcome_trait`	A trait name, e.g. "Coronary heart disease", leaving `outcome_trait` as `NULL` will return MR information related to a specific `exposure_trait`. NOTE: `exposure_trait` and `outcome_trait` cannot be both `NULL`.
`type`	One in `⁠["confounder", "intermediate", "reverse_intermediate", "collider"]⁠` Refer to the confounder view in web application for details
`pval_threshold`	P-value threshold
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /confounder

Examples

## Not run: 
confounder(exposure_trait = "Body mass index", outcome_trait = "Coronary heart disease")

## End(Not run)
## Not run: 
confounder(exposure_trait = "Body mass index", outcome_trait = "Coronary heart disease")

## End(Not run)

Send a query in Cypher to EpiGraphDB

Description

NOTE: this function is intended for advanced uses. Regular users are recommended to use standard query functions

Usage

cypher(query, mode = c("table", "raw"))
cypher(query, mode = c("table", "raw"))

Arguments

`query`	A Cypher query.
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Examples

## Not run: 
cypher("MATCH (n:Gwas) RETURN n LIMIT 2")

## End(Not run)
## Not run: 
cypher("MATCH (n:Gwas) RETURN n LIMIT 2")

## End(Not run)

Drugs for risk factors

Description

GET /drugs/risk-factors

Usage

drugs_risk_factors(trait, pval_threshold = 1e-08, mode = c("table", "raw"))
drugs_risk_factors(trait, pval_threshold = 1e-08, mode = c("table", "raw"))

Arguments

`trait`	A trait name
`pval_threshold`	P-value threshold
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /drugs/risk-factors

Examples

## Not run: 
drugs_risk_factors(trait = "Body mass index")

## End(Not run)
## Not run: 
drugs_risk_factors(trait = "Body mass index")

## End(Not run)

Genetic correlations between traits

Description

GET /genetic-cor

Usage

genetic_cor(trait, cor_coef_threshold = 0.8, mode = c("table", "raw"))
genetic_cor(trait, cor_coef_threshold = 0.8, mode = c("table", "raw"))

Arguments

`trait`	name of the trait, e.g. "body mass index"
`cor_coef_threshold`	correlation coefficient threshold
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /genetic_cor

Examples

## Not run: 
genetic_cor(trait = "Body mass index") %>%
  dplyr::glimpse()

## End(Not run)

# Use a different threshold
## Not run: 
genetic_cor(trait = "Body mass index", cor_coef_threshold = 0.4) %>%
  dplyr::glimpse()

## End(Not run)
## Not run: 
genetic_cor(trait = "Body mass index") %>%
  dplyr::glimpse()

## End(Not run)

# Use a different threshold
## Not run: 
genetic_cor(trait = "Body mass index", cor_coef_threshold = 0.4) %>%
  dplyr::glimpse()

## End(Not run)

Literature evidence regarding a GWAS trait

Description

GET /literature/gwas

Usage

literature_gwas(trait, semmed_predicate = NULL, mode = c("table", "raw"))
literature_gwas(trait, semmed_predicate = NULL, mode = c("table", "raw"))

Arguments

`trait`	A trait name
`semmed_predicate`	Either NULL which returns entries from all predicates, or a SemMed predicate e.g. "DIAGNOSES" or "ASSOCIATED_WITH"
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /literature/gwas

Examples

## Not run: 
literature_gwas(trait = "Body mass index")

## End(Not run)
## Not run: 
literature_gwas(trait = "Body mass index")

## End(Not run)

Return protein uniprot_id from associated genes

Description

POST /mappings/gene-to-protein

Usage

mappings_gene_to_protein(
  gene_name_list = NULL,
  gene_id_list = NULL,
  by_gene_id = FALSE,
  mode = c("table", "raw")
)
mappings_gene_to_protein(
  gene_name_list = NULL,
  gene_id_list = NULL,
  by_gene_id = FALSE,
  mode = c("table", "raw")
)

Arguments

`gene_name_list`	List of HGNC symbols of the genes (default)
`gene_id_list`	List of Ensembl gene IDs (when `by_gene_id == TRUE`)
`by_gene_id`	Search for gene ids (Ensembl gene IDs) instead of gene names (HGNC symbols)
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from POST /mappings/gene-to-protein

Examples

# By HGNC symbols
## Not run: 
mappings_gene_to_protein(gene_name_list = c("GCH1", "MYOF"))

## End(Not run)

# By Enselbl Ids
## Not run: 
mappings_gene_to_protein(gene_id_list = c("ENSG00000162594", "ENSG00000113302"), by_gene_id = TRUE)

## End(Not run)
# By HGNC symbols
## Not run: 
mappings_gene_to_protein(gene_name_list = c("GCH1", "MYOF"))

## End(Not run)

# By Enselbl Ids
## Not run: 
mappings_gene_to_protein(gene_id_list = c("ENSG00000162594", "ENSG00000113302"), by_gene_id = TRUE)

## End(Not run)

List meta nodes (e.g. Gwas, Gene, etc.)

Description

GET /meta/nodes/list

Usage

meta_nodes_list(mode = c("raw"))
meta_nodes_list(mode = c("raw"))

Arguments

mode

If mode = "table", returns a data frame (a tibble as per tidyverse convention). If mode = "raw", returns a raw response from EpiGraphDB API with minimal parsing done by httr.

Value

Data from GET /meta/nodes/list

Examples

## Not run: 
meta_nodes_list()

## End(Not run)
## Not run: 
meta_nodes_list()

## End(Not run)

List nodes under a meta node

Description

GET /meta/nodes/{meta_node}/list

Usage

meta_nodes_list_node(
  meta_node,
  full_data = TRUE,
  limit = 10,
  offset = 0,
  mode = c("table", "raw")
)
meta_nodes_list_node(
  meta_node,
  full_data = TRUE,
  limit = 10,
  offset = 0,
  mode = c("table", "raw")
)

Arguments

`meta_node`	Name of a meta node (e.g. Gwas). Use `meta_nodes_list` to get the full list of meta nodes.
`full_data`	When False, only return the id and name fields (their specific names differ in specific nodes) for a node. This is useful if you want your queries to return results faster with smaller amount of data requested.
`limit`	Max number of items to retrieve.
`offset`	Number of items to skip. Use `limit` and `offset` in combination to do pagination.
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /meta/nodes/{meta_node}/list

Examples

# List the first 5 Gwas nodes, with only id and name fields
## Not run: 
meta_nodes_list_node(meta_node = "Gwas", full_data = FALSE, limit = 5)

## End(Not run)

# List the 6th - 10th Disease nodes, with full properties
## Not run: 
meta_nodes_list_node(meta_node = "Disease", full_data = TRUE, limit = 5, offset = 0)

## End(Not run)
# List the first 5 Gwas nodes, with only id and name fields
## Not run: 
meta_nodes_list_node(meta_node = "Gwas", full_data = FALSE, limit = 5)

## End(Not run)

# List the 6th - 10th Disease nodes, with full properties
## Not run: 
meta_nodes_list_node(meta_node = "Disease", full_data = TRUE, limit = 5, offset = 0)

## End(Not run)

Search a node by its id field, or its name field

Description

GET /meta/nodes/{meta_node}/search

Usage

meta_nodes_search_node(
  meta_node,
  id = NULL,
  name = NULL,
  limit = 10,
  full_data = TRUE,
  mode = c("table", "raw")
)
meta_nodes_search_node(
  meta_node,
  id = NULL,
  name = NULL,
  limit = 10,
  full_data = TRUE,
  mode = c("table", "raw")
)

Arguments

`meta_node`	Name of a meta node (e.g. Gwas). Use `meta_nodes_list` to get the full list of meta nodes.
`id`	The id field of a node (e.g. "ieu-a-2" for a Gwas). Use EpiGraphDB web UI to get a sense of what those ids are for entities.
`name`	The name field of a node (e.g. "body mass index" for a Gwas). Use EpiGraphDB web UI to get a sense of what those names are for entities.
`limit`	Max number of items to retrieve.
`full_data`	When False, only return the id and name fields (their specific names differ in specific nodes) for a node. This is useful if you want your queries to return results faster with smaller amount of data requested.
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /meta/nodes/{meta_node}/search

Examples

# Search Gwas nodes
## Not run: 
meta_nodes_search_node(meta_node = "Gwas", name = "body mass index")

## End(Not run)
# Search Gwas nodes
## Not run: 
meta_nodes_search_node(meta_node = "Gwas", name = "body mass index")

## End(Not run)

List meta rels (e.g. MR, etc.)

Description

GET /meta/rels/list

Usage

meta_rels_list(mode = c("raw"))
meta_rels_list(mode = c("raw"))

Arguments

mode

If mode = "table", returns a data frame (a tibble as per tidyverse convention). If mode = "raw", returns a raw response from EpiGraphDB API with minimal parsing done by httr.

Value

Data from GET /meta/rels/list

Examples

## Not run: 
meta_rels_list()

## End(Not run)
## Not run: 
meta_rels_list()

## End(Not run)

List relationships under a meta relationship

Description

GET /meta/rels/{meta_rel}/list

Usage

meta_rels_list_rel(meta_rel, limit = 10, offset = 0, mode = c("table", "raw"))
meta_rels_list_rel(meta_rel, limit = 10, offset = 0, mode = c("table", "raw"))

Arguments

`meta_rel`	Name of a meta relationship (e.g. MR). Use `meta_rels_list` to get the full list of meta relationships.
`limit`	Max number of items to retrieve.
`offset`	Number of items to skip. Use `limit` and `offset` in combination to do pagination.
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /meta/rels/{meta_rel}/list

Examples

# List the first 5 MR relationships
## Not run: 
meta_rels_list_rel(meta_rel = "MR_EVE_MR", limit = 5)

## End(Not run)
# List the first 5 MR relationships
## Not run: 
meta_rels_list_rel(meta_rel = "MR_EVE_MR", limit = 5)

## End(Not run)

Return information related to Mendelian Randomisation

Description

GET /mr

Usage

mr(
  exposure_trait = NULL,
  outcome_trait = NULL,
  pval_threshold = 1e-05,
  mode = c("table", "raw")
)
mr(
  exposure_trait = NULL,
  outcome_trait = NULL,
  pval_threshold = 1e-05,
  mode = c("table", "raw")
)

Arguments

`exposure_trait`	A trait name, e.g. "Body mass index", leaving `exposure_trait` as `NULL` will return MR information related to a specific `outcome`. NOTE: `exposure_trait` and `outcome_trait` cannot be both `NULL`.
`outcome_trait`	A trait name, e.g. "Coronary heart disease", leaving `outcome_trait` as `NULL` will return MR information related to a specific `exposure_trait`. NOTE: `exposure_trait` and `outcome_trait` cannot be both `NULL`.
`pval_threshold`	P-value threshold
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /mr

Examples

# Returns a data frame
## Not run: 
mr(exposure_trait = "Body mass index", outcome_trait = "Coronary heart disease")

## End(Not run)

# Returns raw response
## Not run: 
mr(
  exposure_trait = "Body mass index", outcome_trait = "Coronary heart disease",
  mode = "raw"
) %>% str()

## End(Not run)

# Use a different threshold
## Not run: 
mr(exposure_trait = "Body mass index", pval_threshold = 1e-8)

## End(Not run)
# Returns a data frame
## Not run: 
mr(exposure_trait = "Body mass index", outcome_trait = "Coronary heart disease")

## End(Not run)

# Returns raw response
## Not run: 
mr(
  exposure_trait = "Body mass index", outcome_trait = "Coronary heart disease",
  mode = "raw"
) %>% str()

## End(Not run)

# Use a different threshold
## Not run: 
mr(exposure_trait = "Body mass index", pval_threshold = 1e-8)

## End(Not run)

Observational correlations between traits

Description

GET /obs-cor

Usage

obs_cor(trait, cor_coef_threshold = 0.8, mode = c("table", "raw"))
obs_cor(trait, cor_coef_threshold = 0.8, mode = c("table", "raw"))

Arguments

`trait`	name of the trait, e.g. "body mass index"
`cor_coef_threshold`	correlation coefficient threshold
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /obs-cor

Examples

## Not run: 
obs_cor(trait = "Body mass index (BMI)") %>%
  dplyr::glimpse()

## End(Not run)

# Use a different threshold
## Not run: 
obs_cor(trait = "Body mass index (BMI)", cor_coef_threshold = 0.8) %>%
  dplyr::glimpse()

## End(Not run)
## Not run: 
obs_cor(trait = "Body mass index (BMI)") %>%
  dplyr::glimpse()

## End(Not run)

# Use a different threshold
## Not run: 
obs_cor(trait = "Body mass index (BMI)", cor_coef_threshold = 0.8) %>%
  dplyr::glimpse()

## End(Not run)

Ontology association between EFO term and Gwas

Description

GET /ontology/gwas-efo

Usage

ontology_gwas_efo(
  trait = NULL,
  efo_term = NULL,
  fuzzy = TRUE,
  mode = c("table", "raw")
)
ontology_gwas_efo(
  trait = NULL,
  efo_term = NULL,
  fuzzy = TRUE,
  mode = c("table", "raw")
)

Arguments

`trait`	trait name, e.g. "body mass"
`efo_term`	EFO term, e.g. "systolic blood pressure"
`fuzzy`	whether query with exact matching (FALSE) or fuzzy matching (default, TRUE)
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /ontology/gwas-efo

Examples

## Not run: 
ontology_gwas_efo(trait = "blood", fuzzy = FALSE)

## End(Not run)

## Not run: 
ontology_gwas_efo(efo_term = "blood pressure", fuzzy = FALSE)

## End(Not run)
## Not run: 
ontology_gwas_efo(trait = "blood", fuzzy = FALSE)

## End(Not run)

## Not run: 
ontology_gwas_efo(efo_term = "blood pressure", fuzzy = FALSE)

## End(Not run)

Pathway evidence

Description

GET /pathway

Usage

pathway(trait, pval_threshold = 1e-05, mode = c("table", "raw"))
pathway(trait, pval_threshold = 1e-05, mode = c("table", "raw"))

Arguments

`trait`	A trait name
`pval_threshold`	P-value threshold
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /pathway

Examples

## Not run: 
pathway(trait = "Body mass index")

## End(Not run)
## Not run: 
pathway(trait = "Body mass index")

## End(Not run)

Return information related to the pQTL analysis

Description

⁠GET /pqtl/⁠

Usage

pqtl(
  query,
  rtype = c("mrres", "simple", "sglmr", "inst", "sense"),
  pvalue = 0.05,
  searchflag = c("traits", "proteins"),
  mode = c("table", "raw")
)
pqtl(
  query,
  rtype = c("mrres", "simple", "sglmr", "inst", "sense"),
  pvalue = 0.05,
  searchflag = c("traits", "proteins"),
  mode = c("table", "raw")
)

Arguments

`query`	(Required) A protein coding gene name or a trait name, e.g. "ADAM19" or "Inflammatory bowel disease" which cannot be `NULL`.
`rtype`	(Optional) A type of data to be extracted, which can be one of these options: `simple`: Basic summary `mrres`: MR results (DEFAULT) `sglmr`: Single SNP MR results `inst`: SNP information `sense`: Sensitivity analysis NOTE: `mrres` is a DEFAULT option.
`pvalue`	(Optional) A pvalue threshold for MR results with the DEFAULT set to 0.05. NOTE: this threshold applies to any `rtype` chosen.
`searchflag`	(Required) A flag to indicate whether you are searching for proteins or traits which cannot be `NULL`. If `query` is a protein name, then this flag should be "proteins"; if `query` is a trait, this flag should be "traits". NOTE: if the wrong flag is chosen for `query`, there will be no result returned.
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from ⁠GET /pqtl/⁠

Examples

# Returns a data frame of MR results, while searching for proteins
## Not run: 
pqtl(query = "ADAM19", searchflag = "proteins")

## End(Not run)

# Returns a data frame with SNP information, while searching for traits
## Not run: 
pqtl(
  query = "Inflammatory bowel disease",
  rtype = "inst",
  searchflag = "traits"
)

## End(Not run)

# Change a pvalue threshold (the default is 0.05)
## Not run: 
pqtl(
  query = "Inflammatory bowel disease",
  rtype = "inst",
  pvalue = 1.0,
  searchflag = "traits"
)

## End(Not run)

# Returns raw response if mode="raw"
## Not run: 
pqtl(
  query = "ADAM19", searchflag = "proteins",
  mode = "raw"
) %>% str()

## End(Not run)
# Returns a data frame of MR results, while searching for proteins
## Not run: 
pqtl(query = "ADAM19", searchflag = "proteins")

## End(Not run)

# Returns a data frame with SNP information, while searching for traits
## Not run: 
pqtl(
  query = "Inflammatory bowel disease",
  rtype = "inst",
  searchflag = "traits"
)

## End(Not run)

# Change a pvalue threshold (the default is 0.05)
## Not run: 
pqtl(
  query = "Inflammatory bowel disease",
  rtype = "inst",
  pvalue = 1.0,
  searchflag = "traits"
)

## End(Not run)

# Returns raw response if mode="raw"
## Not run: 
pqtl(
  query = "ADAM19", searchflag = "proteins",
  mode = "raw"
) %>% str()

## End(Not run)

Return a list of all proteins/exposures or traits/outcomes available in the database

Description

⁠GET /pqtl/list/⁠

Usage

pqtl_list(flag = c("exposures", "outcomes"), mode = c("table", "raw"))
pqtl_list(flag = c("exposures", "outcomes"), mode = c("table", "raw"))

Arguments

`flag`	(Optional) A flag which indicates whether the list of exposures (if "exposures") or outcomes (if "outcomes") should be returned. The DEFAULT is "exposures".
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from ⁠GET /pqtl/list/⁠

Examples


# Returns a list of available proteins (exposures)
## Not run: 
pqtl_list()

## End(Not run)

# Returns a list of available traits (outcomes)
## Not run: 
pqtl_list(flag = "outcomes")

## End(Not run)
# Returns a list of available proteins (exposures)
## Not run: 
pqtl_list()

## End(Not run)

# Returns a list of available traits (outcomes)
## Not run: 
pqtl_list(flag = "outcomes")

## End(Not run)

Return information related to the pleiotropy of SNPs

Description

⁠GET /pqtl/pleio/⁠

Usage

pqtl_pleio(
  rsid = NULL,
  prflag = c("proteins", "count"),
  mode = c("table", "raw")
)
pqtl_pleio(
  rsid = NULL,
  prflag = c("proteins", "count"),
  mode = c("table", "raw")
)

Arguments

`rsid`	(Required) A SNP identified by rsID which cannot be `NULL`.
`prflag`	(Optional) A flag which determines whether the number (if "count") or names (if "proteins") of the associated proteins should be returned. The DEFAULT value is "proteins".
`mode`	(Optional) If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from ⁠GET /pqtl/pleio/⁠

Examples


# Returns a data frame of associated proteins
## Not run: 
pqtl_pleio(rsid = "rs1260326")

## End(Not run)

# Returns a number of associated proteins
## Not run: 
pqtl_pleio(rsid = "rs1260326", prflag = "count")

## End(Not run)
# Returns a data frame of associated proteins
## Not run: 
pqtl_pleio(rsid = "rs1260326")

## End(Not run)

# Returns a number of associated proteins
## Not run: 
pqtl_pleio(rsid = "rs1260326", prflag = "count")

## End(Not run)

For the list of proteins, returns their associated pathway data

Description

⁠POST /protein/in-pathway⁠

Usage

protein_in_pathway(uniprot_id_list, mode = c("table", "raw"))
protein_in_pathway(uniprot_id_list, mode = c("table", "raw"))

Arguments

`uniprot_id_list`	A list of protein UniProt IDs
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from ⁠POST /protein/in-pathway⁠

Examples

## Not run: 
protein_in_pathway(uniprot_id_list = c("014933", "060674", "P32455"))

## End(Not run)
## Not run: 
protein_in_pathway(uniprot_id_list = c("014933", "060674", "P32455"))

## End(Not run)

Send data request to an EpiGraphDB API endpoint

Description

This is a general purpose function to send data request which can be used when there has not been an R equivalent package function to an API endpoint. Underneath this is a wrapper around httr functions with better handling of returned status.

Usage

query_epigraphdb(
  route,
  params = NULL,
  mode = c("raw", "table"),
  method = c("GET", "POST"),
  retry_times = 3,
  retry_pause_min = 1
)
query_epigraphdb(
  route,
  params = NULL,
  mode = c("raw", "table"),
  method = c("GET", "POST"),
  retry_times = 3,
  retry_pause_min = 1
)

Arguments

`route`	An EpiGraphDB API endpoint route, e.g. `"/mr"` or `"/confounder"`. Consult the EpiGraphDB API documentation.
`params`	A list of parameters associated with the query endpoint.
`mode`	`c("raw", "table")`, if `"table"` then the query handler will try to convert the returned data to a tibble dataframe. NOTE: The default mode is "raw" which will NOT convert the returned response to a dataframe. This is different to functions that query topic endpoints which default to return a dataframe. Explicitly specify `mode = "table"` when needed.
`method`	Type of HTTP (GET, POST, PUT, etc.) method. NOTE: When sending a POST request where a specific parameter is specified as a list on the API, and if the equivalent in R is a vector of length 1, you should wrap this parameter in `I()`, e.g. I(c("APOE")) to avoid auto unboxing. For details, please refer to `httr::POST`
`retry_times`	Number of times the function will retry the request to the API.
`retry_pause_min`	Minimum number of seconds to wait for the next retry.

Value

Data from an EpiGraphDB API endpoint.

Examples

# GET /mr
# equivalent to `mr(exposure_trait = "Body mass index", outcome_trait = "Coronary heart disease")`
## Not run: 
query_epigraphdb(
  route = "/mr",
  params = list(
    exposure_trait = "Body mass index",
    outcome_trait = "Coronary heart disease"
  ),
  mode = "table"
)

## End(Not run)

# GET /meta/nodes/Gwas/list
## Not run: 
query_epigraphdb(
  route = "/meta/nodes/Gwas/list",
  params = list(
    limit = 5,
    offset = 0
  )
) %>% str(1)

## End(Not run)

# POST /protein/ppi
## Not run: 
query_epigraphdb(
  route = "/protein/ppi",
  params = list(
    uniprot_id_list = c("P30793", "Q9NZM1", "O95236")
  ),
  method = "POST"
)

## End(Not run)

# error handling
## Not run: 
tryCatch(
  query_epigraphdb(
    route = "/mr",
    params = list(
      exposure_trait = NULL,
      outcome_trait = NULL
    ),
    retry_times = 0
  ),
  error = function(e) {
    message(e)
  }
)

## End(Not run)
# GET /mr
# equivalent to `mr(exposure_trait = "Body mass index", outcome_trait = "Coronary heart disease")`
## Not run: 
query_epigraphdb(
  route = "/mr",
  params = list(
    exposure_trait = "Body mass index",
    outcome_trait = "Coronary heart disease"
  ),
  mode = "table"
)

## End(Not run)

# GET /meta/nodes/Gwas/list
## Not run: 
query_epigraphdb(
  route = "/meta/nodes/Gwas/list",
  params = list(
    limit = 5,
    offset = 0
  )
) %>% str(1)

## End(Not run)

# POST /protein/ppi
## Not run: 
query_epigraphdb(
  route = "/protein/ppi",
  params = list(
    uniprot_id_list = c("P30793", "Q9NZM1", "O95236")
  ),
  method = "POST"
)

## End(Not run)

# error handling
## Not run: 
tryCatch(
  query_epigraphdb(
    route = "/mr",
    params = list(
      exposure_trait = NULL,
      outcome_trait = NULL
    ),
    retry_times = 0
  ),
  error = function(e) {
    message(e)
  }
)

## End(Not run)

Multi SNP QTL MR evidence

Description

GET /xqtl/multi-snp-mr

Usage

xqtl_multi_snp_mr(
  exposure_gene = NULL,
  outcome_trait = NULL,
  mr_method = c("IVW", "Egger"),
  qtl_type = c("eQTL", "pQTL"),
  pval_threshold = 1e-05,
  mode = c("table", "raw")
)
xqtl_multi_snp_mr(
  exposure_gene = NULL,
  outcome_trait = NULL,
  mr_method = c("IVW", "Egger"),
  qtl_type = c("eQTL", "pQTL"),
  pval_threshold = 1e-05,
  mode = c("table", "raw")
)

Arguments

`exposure_gene`	Name of the exposure gene
`outcome_trait`	Name of the outcome trait
`mr_method`	"IVW" or "Egger"
`qtl_type`	"eQTL" or "pQTL"
`pval_threshold`	P-value threshold
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GET /xqtl/multi-snp-mr

Examples

## Not run: 
xqtl_multi_snp_mr(outcome_trait = "Coronary heart disease")

## End(Not run)
## Not run: 
xqtl_multi_snp_mr(outcome_trait = "Coronary heart disease")

## End(Not run)

Single SNP QTL MR evidence

Description

GET /xqtl/single-snp-mr

Usage

xqtl_single_snp_mr(
  exposure_gene = NULL,
  outcome_trait = NULL,
  snp = NULL,
  qtl_type = c("eQTL", "pQTL"),
  pval_threshold = 1e-05,
  mode = c("table", "raw")
)
xqtl_single_snp_mr(
  exposure_gene = NULL,
  outcome_trait = NULL,
  snp = NULL,
  qtl_type = c("eQTL", "pQTL"),
  pval_threshold = 1e-05,
  mode = c("table", "raw")
)

Arguments

`exposure_gene`	Name of the exposure gene
`outcome_trait`	Name of the outcome trait
`snp`	SNP rsid
`qtl_type`	"eQTL" or "pQTL"
`pval_threshold`	P-value threshold
`mode`	If `mode = "table"`, returns a data frame (a `tibble` as per `tidyverse` convention). If `mode = "raw"`, returns a raw response from EpiGraphDB API with minimal parsing done by `httr`.

Value

Data from GEET /xqtl/single-snp-mr

Examples

## Not run: 
xqtl_single_snp_mr(outcome_trait = "Coronary heart disease")

## End(Not run)
## Not run: 
xqtl_single_snp_mr(outcome_trait = "Coronary heart disease")

## End(Not run)

Package 'epigraphdb'

Help Index

MR evidence on confounding traits between exposure and outcome

Description

Usage

Arguments

Value

Examples

Send a query in Cypher to EpiGraphDB

Description

Usage

Arguments

Examples

Drugs for risk factors

Description

Usage

Arguments

Value

Examples

Genetic correlations between traits

Description

Usage

Arguments

Value

Examples

Literature evidence regarding a GWAS trait

Description

Usage

Arguments

Value

Examples

Return protein uniprot_id from associated genes

Description

Usage

Arguments

Value

Examples

List meta nodes (e.g. Gwas, Gene, etc.)

Description

Usage

Arguments

Value

Examples

List nodes under a meta node

Description

Usage

Arguments

Value

Examples

Search a node by its id field, or its name field

Description

Usage

Arguments

Value

Examples

List meta rels (e.g. MR, etc.)

Description

Usage

Arguments

Value

Examples

List relationships under a meta relationship

Description

Usage

Arguments

Value

Examples

Return information related to Mendelian Randomisation

Description

Usage

Arguments

Value

Examples

Observational correlations between traits

Description

Usage

Arguments

Value

Examples

Ontology association between EFO term and Gwas