gap (version 1.1-2)

asplot: Regional association plot

Description

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

Note that the best p value is not necessarily within locus in the original design.

Usage

asplot(snp, locusname, chr, locus, gmap, glist, best.pval=NULL, sf=c(3,8), logpmax=9, pch=23)

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 with columns c("POS", "PVAL", "TYPE", "RSQR"), row.names(locus) contains the SNP name, e.g., snp

gmap

The genetic map, e.g., c("position","COMBINED_rate.cM.Mb.","Genetic_Map.cM.")

glist

The gene annotation with columns c("START", "STOP", "SIZE", "STRAND", "GENE")

best.pval

The best p value for the locus of interest

sf

scale factors for p values and recombination rates, smaller values are necessary for gene dense regions

logpmax

The maximum value for -log10(p)

pch

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

References

DGI. Whole-genome association analysis identifies novel loci for type 2 diabetes and triglyceride levels. Science 2007;316(5829):1331-6

Examples

asplot("rs10811661", "CDKN2A/CDKN2B region", "9", CDKNlocus, CDKNmap, CDKNgenes)
asplot("rs10811661", "CDKN2A/CDKN2B region", "9", CDKNlocus, CDKNmap, CDKNgenes, 5.4e-8, c(3,6))