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 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

Author(s)

Paul de Bakker, Jing Hua Zhao, Shengxu Li

Examples

## Not run: 
asplot("rs10811661", "CDKN2A/CDKN2B region", "9", CDKNlocus, CDKNmap, CDKNgenes)
asplot("rs10811661", "CDKN2A/CDKN2B region", "9", CDKNlocus, CDKNmap, CDKNgenes, 5.4e-8, c(3,6))
## End(Not run)

[Package gap version 1.0-17 Index]