Package 'GWASapi'

Check if the GWAS Catalog is live

Description

Check if the GWAS Catalog is live

Usage

check_gwasapi()

Value

Character string.

Examples

check_gwasapi()

---

Get GWAS associations for a given region

Description

Get GWAS associations for a given region

Usage

get_asso(
  chr,
  bp_lower = NULL,
  bp_upper = NULL,
  study = NULL,
  p_lower = NULL,
  p_upper = NULL,
  start = NULL,
  size = NULL
)

Arguments

chr	chromosome number
bp_lower	Lower endpoint of basepairs initerval
bp_upper	Upper endpoint of basepairs initerval
study	Restrict to a particular study
p_lower	Lower bound on p-values
p_upper	Upper bound of p-values
start	First record to retrieve (starting at 0)
size	Maximum number of results to retrieve

Value

Data frame of associations

See Also

get_variant(), get_trait_asso()

Examples

result <- get_asso(chr=19, bp_lower=19200000, bp_upper=19300000)

---

Get GWAS associations for a particular trait

Description

Get GWAS associations for a particular trait

Usage

get_trait_asso(
  trait = NULL,
  study = NULL,
  p_lower = NULL,
  p_upper = NULL,
  start = NULL,
  size = NULL
)

Arguments

trait	Restrict to a particular study
study	Restrict to a particular study
p_lower	Lower bound on p-values
p_upper	Upper bound of p-values
start	First record to retrieve (starting at 0)
size	Maximum number of results to retrieve

Value

Data frame of associations

See Also

get_variant(), get_asso()

Examples

## Not run: result <- get_trait_asso("EFO_0001360", p_upper=1e-10)

---

Get associations for a given variant

Description

Get all associations for a given variant

Usage

get_variant(
  rsnum,
  chr = NULL,
  p_lower = NULL,
  p_upper = NULL,
  study = NULL,
  start = NULL,
  size = NULL
)

Arguments

rsnum	RS number for a variant
chr	chromosome number if known
p_lower	Lower bound on p-values
p_upper	Upper bound of p-values
study	Restrict to a particular study
start	First record to retrieve (starting at 0)
size	Maximum number of results to retrieve

Value

Data frame with associations as rows

See Also

get_asso(), get_trait_asso()

Examples

# get associations for a given variant
results <- get_variant("rs2228603")
# use information about the chromosome it's on
results <- get_variant("rs2228603", 19)
# get the next 20 results
next20 <- get_variant("rs2228603", 19, start=20)
# get 100 results rather than just 20
first100 <- get_variant("rs2228603", 19, size=100)
# return just the associations with P < 1e-8
top_results <- get_variant("rs2228603", 19, p_upper=1e-8)

---

Information about a study

Description

Information about a particular study

Usage

info_study(study)

Arguments

study

Study identifieer

Value

List of meta-data

---

List chromosomes

Description

List chromosomes

Usage

list_chr()

Value

Vector of chromosome numbers (as integers)

See Also

list_studies(), list_traits()

Examples

chr <- list_chr()

---

List studies

Description

List studies

Usage

list_studies(trait = NULL, start = NULL, size = NULL)

Arguments

trait	If provided, restrict search to studies that included the specified trait.
start	First record to retrieve (starting at 0)
size	Maximum number of results to retrieve

Value

Vector of study accessions

See Also

list_chr(), list_traits()

Examples

first20 <- list_studies() # returns 20 studies
next20 <- list_studies(start=20) # returns the next 20 studies
first100 <- list_studies(size=100) # returns 100 studies
with_trait <- list_studies(trait="EFO_0001360")

---

List traits

Description

List traits

Usage

list_traits(start = NULL, size = NULL)

Arguments

start	First record to retrieve (starting at 0)
size	Maximum number of results to retrieve

Value

Vector of trait IDs

See Also

list_studies(), list_chr()

Examples

first20 <- list_traits() # first 20 traits
next20 <- list_traits(start=20) # the next 20 traits
first100 <- list_traits(size=100) # returns 100 traits

---