sentinels {gap}R Documentation

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

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.

Value

The function give screen output.

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)
}

## End(Not run)

[Package gap version 1.2.1 Index]