eQTL-specific analysis — xQTLanalyze_propensity • xQTLbiolinks

eQTL-specific analysis

xQTLanalyze_propensity(
  gene = "",
  geneType = "auto",
  variantName = "",
  variantType = "auto",
  tissueLabels = "",
  study = "",
  population = "EUR"
)

Arguments

gene: (character) gene symbol or gencode id (versioned or unversioned are both supported).
geneType: (character) options: "auto","geneSymbol" or "gencodeId". Default: "auto".
variantName: (character) name of variant, dbsnp ID and variant id is supported, eg. "rs138420351" and "chr17_7796745_C_T_b38".
variantType: (character) options: "auto", "snpId" or "variantId". Default: "auto".
tissueLabels: (a character vector) can be listed with ebi_study_tissues. If is null, use all tissue / cell-types. (Default)
study: (character) Studies can be listed using ebi_study_tissues. If is null, use all studies (Default).
population: (string) One of the 5 popuations from 1000 Genomes: 'AFR', 'AMR', 'EAS', 'EUR', and 'SAS'.

Value

A list containing four data.table objects, including: "snpLD" for LD details of the specified SNP; "assoAllLd" for eQTL details of LD-associated SNPs; "lm_R2_logP" for liner regression results; "cor_R2_logP" for correlation outputs;

Examples

# \donttest{
propensityRes <- xQTLanalyze_propensity( gene="MMP7", variantName="rs11568818", study="TwinsUK")
# propensityRes <- xQTLanalyze_propensity(gene="FLOT1", variantName="rs3130356", study="")
xQTLvisual_qtlPropensity(propensityRes)
# }