asplot {gap} | R Documentation |
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.
asplot(snp, locusname, chr, locus, gmap, glist, best.pval=NULL, sf=c(3,8), logpmax=9, pch=23)
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 |
DGI. Whole-genome association analysis identifies novel loci for type 2 diabetes and triglyceride levels. Science 2007;316(5829):1331-6
Paul de Bakker, Jing Hua Zhao, Shengxu Li
## 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)