asplot {gap}R Documentation

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

Author(s)

Paul de Bakker, Jing Hua Zhao

Examples

## Not run: 
data(CDKN)
asplot("rs10811661", "CDKN2A/CDKN2B region", "9", CDKNlocus, 9, 5.4e-8, 23, CDKNmap, CDKNgenes)
## End(Not run)

[Package gap version 1.0-15 Index]