sentinels {gap} | R Documentation |
This function accepts an object containing GWAS summary statistics for signal identification as defined by flanking regions.
sentinels(p,st,debug=FALSE,flanking=1e+6)
p |
an object containing GWAS summary statistics |
st |
row number as in p |
debug |
a flag to show the actual data |
flanking |
the width of flanking region |
Typically, input to the function are variants reaching certain level of significance and the functtion identifies minimum p value at the flanking interval; in the case of another variant in the flanking window has smaller p value then it will be replaced.
The function give screen output.
## Not run: # prot is the phenotype # tag features data specifics, e.g., HLA prot <- Sys.getenv("prot") tag <- Sys.getenv("tag") p <- read.delim(paste0("work/",prot,tag,".p"),as.is=TRUE) chrs <- with(p,unique(Chrom)) for(chr in chrs) { ps <- subset(p,Chrom==chr) row.names(ps) <- 1:nrow(ps) pp(ps, 1) } ## End(Not run)