In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

knitr::opts_chunk$set(echo = TRUE)

Creating the resources

library(opalr)
o <- opal.login("administrator","password", 
                url="https://opal-demo.obiba.org")
url <- dsOmicsClient::get_EGA_url("EGAF00004199964", 3, 1000, 10000)
opal.project_create(o, "EGA")
opal.resource_create(o, "EGA", "EGA_vcf_EGAF00004199964", 
  url = url, 
  format = "EGAhtsgetVCF", 
  identity = "[e-mail]",
  secret = "egarocks",
  package = "dsOmics")
opal.resource_create(o, "EGA", "EGA_vcf_EGAF00004199964_phenotypes", 
  url = "https://raw.githubusercontent.com/isglobal-brge/brgedata/master/data/ega_synthetic_data_phenotypes.csv", 
  format = "csv")

# to test the resource assignment
opal.assign.resource(o, "client", "EGA.EGA_vcf_EGAF00004199964")
opal.assign.resource(o, "client", "EGA.EGA_vcf_EGAF00004199964_phenotypes")
opal.execute(o, "class(client)")
opal.logout(o)

Analysis

library(DSOpal)
library(dsBaseClient)
library(dsOmicsClient)

# prepare login data and resource to assign
builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1", url = "https://opal-demo.obiba.org", 
               user = "dsuser", password = "password", 
               resource = "EGA.EGA_vcf_EGAF00004199964_phenotypes", driver = "OpalDriver")
logindata <- builder$build()

# login and assign resource
conns <- DSI::datashield.login(logins = logindata, assign = TRUE, 
                               symbol = "res")
datashield.assign.expr(conns, symbol = "D", 
                       expr = quote(as.resource.data.frame(res)))
datashield.assign.resource(conns, symbol = 'gen_vcf', resource = list(study1 = 'EGA.EGA_vcf_EGAF00004199964'))
datashield.assign.expr(conns, symbol = "gds", 
                       expr = quote(as.resource.object(gen_vcf)))
datashield.logout(conns)

PCA

Allele Frequency

Association SNP to Phenotype

Stratified Association SNP to Phenotype

Same pero amb regió (Genomic Ranges)

GWAS

isglobal-brge/dsOmicsClient documentation built on March 20, 2023, 3:52 p.m.