find_proxy

find_proxy finds the proxy snp for the miss iv

Usage

find_proxy(
  miss_iv,
  miss_snp,
  outcome_snp,
  proxy_file = NULL,
  proxy_output_path = NULL,
  pop = "EUR",
  gb = "grch38",
  token = ""
)

Arguments

miss_iv

iv datafram in tsmr exposure format, which can not locate snp in the outcome

miss_snp

snp in the miss_iv; can be inferred using miss_iv$SNP

outcome_snp

a str vector containing all snp in the outcome; this NOT the entire outcome gwas summary statistics

proxy_file

pre-calculated proxy file path (full); do provide this if the proxy file is already generated !!!

proxy_output_path

a full path to save the proxy file when using ldlink

pop

reference panel from 1kg (LDlinkR param)

gb

genome build (LDlinkR param)

token

token of LDlinkR

Value

a updated missiv with proxy.snp proxy.effect.allele proxy.other.allele r2 col

Examples

# This function can be used when many iv can not locate corresponding snp in the outcome
# in tsmr analysis
if (FALSE) { # \dontrun{
# iv is estracted iv via tsmr package;dat_h is a standard output of harmonise_data()
miss_iv <- iv[!iv$SNP %in% dat_h$SNP,]
miss_snp <- miss_iv$SNP
outcome_snp <- iri_nc$SNP
proxy_output_path <- "Full path to where you wanna store the LDlinkR output"
 proxy_iv <- find_proxy(miss_iv, miss_snp, outcome_snp,
                        proxy_file = "./combined_query_snp_list_grch38.txt",
                        proxy_output_path = NULL)
 # bak
 proxy_iv$target.snp <- proxy_iv$SNP # target snp
 proxy_iv$target.A1 <- proxy_iv$effect_allele.exposure
 proxy_iv$target.A2 <- proxy_iv$other_allele.exposure
 # replace for tsmr
 proxy_iv$SNP <- proxy_iv$proxy.snp
 proxy_iv$effect_allele.exposure <- proxy_iv$proxy.A1
 proxy_iv$other_allele.exposure <- proxy_iv$proxy.A2
 iv_f <- bind_rows(non_miss_iv, proxy_iv) # f for final
 dat_h_proxy <- harmonise_data(iv_f, out_nc_proxy)
 mr(dat_h_proxy) # nailed it!
} # }