| 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)