asplot {gap} | R Documentation |
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.
asplot(snp, locusname, chr, locus, range, best.pval, pch, recomb, genelist)
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 |
Paul de Bakker, Jing Hua Zhao
## Not run: data(CDKN) asplot("rs10811661", "CDKN2A/CDKN2B region", "9", CDKNlocus, 9, 5.4e-8, 23, CDKNmap, CDKNgenes) ## End(Not run)