epigraphdb (version 0.2.3)

pqtl: 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")
)

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:

1. simple: Basic summary

2. mrres: MR results (DEFAULT)

3. sglmr: Single SNP MR results

4. inst: SNP information

5. 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

# NOT RUN {
# Returns a data frame of MR results, while searching for proteins
# }
# NOT RUN {
pqtl(query = "ADAM19", searchflag = "proteins")
# }
# NOT RUN {
# Returns a data frame with SNP information, while searching for traits
# }
# NOT RUN {
pqtl(
  query = "Inflammatory bowel disease",
  rtype = "inst",
  searchflag = "traits"
)
# }
# 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"
)
# }
# NOT RUN {
# Returns raw response if mode="raw"
# }
# NOT RUN {
pqtl(
  query = "ADAM19", searchflag = "proteins",
  mode = "raw"
) %>% str()
# }