EbiDataset: Object that downloads, develops and uploads EBI dataset

In MRCIEU/EbiDataImport: Import EBI Data to OpenGWAS

Object that downloads, develops and uploads EBI dataset

Description

Object that downloads, develops and uploads EBI dataset

Object that downloads, develops and uploads EBI dataset

Super class

GwasDataImport::Dataset -> EbiDataset

Public fields

ebi_id

EBI ID to look for

traitname

Name of trait

ftp_path

Path to files in EBI FTP

or_flag

TRUE/FALSE if had to convert OR to beta

gwas_out1

Path to first look at EBI dataset

Methods

Public methods

• EbiDataset$new()

• EbiDataset$download_dataset()

• EbiDataset$format_ebi_dataset()

• EbiDataset$organise_metadata()

• EbiDataset$pipeline()

• EbiDataset$clone()

Inherited methods

• GwasDataImport::Dataset$api_gwas_release()
• GwasDataImport::Dataset$api_gwasdata_check()
• GwasDataImport::Dataset$api_gwasdata_delete()
• GwasDataImport::Dataset$api_gwasdata_upload()
• GwasDataImport::Dataset$api_metadata_check()
• GwasDataImport::Dataset$api_metadata_delete()
• GwasDataImport::Dataset$api_metadata_edit()
• GwasDataImport::Dataset$api_metadata_upload()
• GwasDataImport::Dataset$api_qc_status()
• GwasDataImport::Dataset$api_report()
• GwasDataImport::Dataset$check_meta_data()
• GwasDataImport::Dataset$collect_metadata()
• GwasDataImport::Dataset$delete_wd()
• GwasDataImport::Dataset$determine_columns()
• GwasDataImport::Dataset$format_dataset()
• GwasDataImport::Dataset$get_gwasdata_fields()
• GwasDataImport::Dataset$get_metadata_fields()
• GwasDataImport::Dataset$is_new_id()
• GwasDataImport::Dataset$se_from_bp()
• GwasDataImport::Dataset$set_wd()
• GwasDataImport::Dataset$view_metadata_options()
• GwasDataImport::Dataset$write_metadata()

---

Method new()

Initialise object

Usage

EbiDataset$new(
  ebi_id,
  wd = tempdir(),
  ftp_path = NULL,
  igd_id = paste0("ebi-a-", ebi_id),
  traitname = NULL
)

Arguments

ebi_id

e.g. GCST005522

wd

Directory in which to download and develop dataset. Default=tempdir(). Deleted automatically upon object removal

ftp_path

Pre-specified path to data. Default=NULL

igd_id

Defaults to "ebi-a-<ebi_id>"

traitname

Option to provide traitname of dataset

Returns

A new EbiDataset object

---

Method download_dataset()

Download

Usage

EbiDataset$download_dataset(
  ftp_path = self$ftp_path,
  ftp_url = options()$ebi_ftp_url,
  outdir = self$wd
)

Arguments

ftp_path

Pre-specified path to data. Default=self$ftp_path

ftp_url

Default=options()$ebi_ftp_url

outdir

Default=self$wd

---

Method format_ebi_dataset()

organise data before formatting. This is slow but doesn't really matter

Usage

EbiDataset$format_ebi_dataset(
  filename = self$filename,
  output = file.path(self$wd, "step1.txt.gz")
)

Arguments

filename

Filename of GWAS dataset

output

Where to save formatted dataset

---

Method organise_metadata()

Download and parse metadata

Usage

EbiDataset$organise_metadata(
  ebi_id = self$ebi_id,
  or_flag = self$or_flag,
  igd_id = self$igd_id,
  units = NULL,
  sex = "NA",
  category = "NA",
  subcategory = "NA",
  build = "HG19/GRCh37",
  group_name = "public",
  traitname = self$traitname
)

Arguments

ebi_id

Default=self$ebi_id

or_flag

Default=self$or_flag

igd_id

Default=NULL

units

Default=NULL

sex

Default="NA"

category

Default="NA"

subcategory

Default="NA"

build

Default="HG19/GRCh37"

group_name

Default="public"

traitname

Default=self$traitname

---

Method pipeline()

Once initialised this function will string together everything i.e. downloading, processing and uploading

Usage

EbiDataset$pipeline()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

EbiDataset$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

MRCIEU/EbiDataImport documentation built on May 9, 2023, 6 a.m.