gap (version 1.0-15)

asplot: Regional association plot

Description

This function obtains regional association plot for a particular locus, based on the information about recombinatino rates, linkage disequilibrium between the SNP of interest and neighbouring ones, and single-point association tests p values.

Usage

asplot(snp, locusname, chr, locus, range, best.pval, pch, recomb, genelist)

Arguments

snp

The SNP name, e.g., "rs10811661"

locusname

The classic term for locus where a gene locates

chr

The name of the chromosome, e.g., "1", ..., "X"

locus

The data frame containing association results

range

The range for -log10(p), e.g., 9

best.pval

The best p value for the locus of interest

pch

Plotting character for the SNPs to be highlighted, e.g., 21 and 23 refer to circle and diamond

recomb

The genetic map

genelist

The gene annotation

Examples

data(CDKN)
asplot("rs10811661", "CDKN2A/CDKN2B region", "9", CDKNlocus, 9, 5.4e-8, 23, CDKNmap, CDKNgenes)