gap (version 1.2.1)

sentinels: Sentinel identification from GWAS summary statistics

Description

This function accepts an object containing GWAS summary statistics for signal identification as defined by flanking regions.

Usage

sentinels(p,st,debug=FALSE,flanking=1e+6)

Arguments

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

Value

The function give screen output.

Details

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.

Examples

# 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)
}
# }