Skip to contents

R/phenoscanner only allows for certain number of items supplied. This simple function return a large number of calls in batches as well as generating SNPIDs.

Usage

snpqueries(
  snplist,
  catalogue = "pQTL",
  proxies = "EUR",
  p = 5e-08,
  r2 = 0.8,
  build = 37,
  wait = TRUE
)

Arguments

snplist

a list of SNPs.

catalogue

"None","eQTL","mQTL","methQTL","pQTL","GWAS".

proxies

"None", "AFR","AMR","EAS","EUR","SAS".

p

p value threshold.

r2

r2 for LD.

build

37, 38.

wait

a flag to wait for 1hr for every 500 SNPs.

Value

The returned value is a list containing snps and results:

Details

Batches are generated and queries are combined into one.

Note

adapted from custom codings

References

Sun BB, et al. (2018). Genomic atlas of the human plasma proteome. Nature 558: 73-79.

See also

Examples

if (FALSE) {
 # single SNP
 snpqueries("rs704")
 # SCALLOP/INF
INF <- Sys.getenv("INF")
rsid <- scan(paste(INF,'work','INF1.merge.snp',sep='/'),"")
r <- snpqueries(rsid,catalogue='pQTL',p=1e-11)
INTERVAL_Olink <- subset(with(r,results),efo=='EFO_0004747' & pmid=='29875488')
save(INTERVAL_Olink,file='INTERVAL_Olink.rda',compress='xz')
# --- query intersect proteins ---
# SomaLogic intersect
SomaLogic_overlap_list <- subset(st4,UniProt %in% intersect_list)
r <- snpqueries(SomaLogic_overlap_list[,6],catalogue='pQTL',p=1e-11)
SomaLogic_overlap <- subset(with(r,results),efo=='EFO_0004747' & pmid=='29875488')
save(SomaLogic_overlap_list,SomaLogic_overlap,file='SomaLogic_overlap.rda',compress='xz')
SomaLogic_result <- merge(SomaLogic_overlap_list,SomaLogic_overlap,
                          by.x="Sentinel.variant*",by.y="snp")
# Olink intersect
INF1_merge_rsid <- read.delim(paste(INF,"work","INF1.merge-rsid",sep="/"))
INF1_merge_rsid_uniprot <- merge(INF1_merge_rsid,inf1,by="prot")
Olink_overlap_list <- subset(INF1_merge_rsid_uniprot,uniprot %in% intersect_list)
r <- snpqueries(with(Olink_overlap_list,MarkerName),catalogue='pQTL',p=1e-11)
Olink_overlap <- subset(with(r,results),efo=='EFO_0004747' & pmid=='29875488')
save(Olink_overlap_list,Olink_overlap,file='Olink_overlap.rda',compress='xz')
Olink_result <- merge(Olink_overlap_list,Olink_overlap,by.x="MarkerName",by.y="snp")
}