Locus novelty check

This function checks novelty of a list of loci such as pQTLs against a published list. Both known_loci and query_loci have these variables: chr, pos, uniprot, rsid, prot.

Usage

novelty_check(
  known_loci,
  query_loci,
  flanking = 1e+06,
  pop = "EUR",
  verbose = TRUE
)

Arguments

known_loci

A data.frame of published loci.

query_loci

A data.frame of loci whose novelties are unclear.

flanking

A flanking distance.

pop

The reference population as for ieugwasr::ld_matrix().

verbose

A flag to show nonexistent variants.

Value

A data.frame containing nonnovel loci.

Examples

if (FALSE) { 
 options(width=2000)
 suppressMessages(require(dplyr))
 # SCALLOP-INF list
 METAL <- read.delim("~/pQTLtools/tests/INF1.METAL") %>%
          mutate(prot_rsid=paste0(uniprot,"-",rsid),pos=Position)
 # UKB_PPP list
 require(openxlsx)
 url <- "~/rds/results/public/proteomics/UKB-PPP/sun22.xlsx"
 ST10 <- read.xlsx(url,"ST10",startRow=3) %>%
         mutate(uniprot=Target.UniProt,rsid=rsID,prot=Assay.Target) %>%
         mutate(prot_rsid=paste0(uniprot,"-",rsid))
 sentinels <- left_join(METAL,ST10,by="prot_rsid") %>%
              select(prot_rsid,cis.trans,rsID) %>%
              filter(!is.na(rsID))
 inf1 <- c(with(pQTLtools::inf1,uniprot),with(METAL,uniprot)) %>%
         unique()
 overlap <- filter(ST10,uniprot %in% inf1)
 dim(overlap)
 UKB_PPP <- mutate(overlap,
            chrpos=strsplit(overlap[["Variant.ID.(CHROM:GENPOS.(hg37):A0:A1:imp:v1)"]],":"),
            chr=lapply(chrpos,"[[",1),
            pos=lapply(chrpos,"[[",2),
            chrpos=paste(chr,pos,sep=":"))
 suppressMessages(require(GenomicRanges))
 b <- novelty_check(UKB_PPP,METAL)
 replication <- filter(b,r2>=0.8)
 # Mutual uses of pQTLtools/SCALLOP-INF
 write.table(replication,file="~/INF/work/UKB-PPP.txt",row.names=FALSE,quote=FALSE,sep="\t")
 load("~/pQTLtools/tests/novel_data.rda")
 prot_rsid <- with(novel_data,paste0(prot,"-",rsid))
 prot_rsid_repl <- with(replication,paste0(query.prot,"-",query.rsid))
 left <- setdiff(prot_rsid,prot_rsid_repl)
}