plots: Visualize of trait-associated SNPs
In traseR: GWAS trait-associated SNP enrichment analyses in genomic intervals

Description Usage Arguments Value Author(s) Examples

These are a group of functions to generate plot to visualize the trait-associated SNPs.

	
plotContext(snpdb, region=NULL, keyword = NULL, pvalue = 1e-3)

plotPvalue(snpdb, region=NULL, keyword = NULL, plot.type = c("densityplot", "boxplot"), pvalue = 1e-3, xymax = 50)

plotSNP(snpdb, snpid, ext = 10000)

plotGene(snpdb, gene, ext = 10000)

plotInterval(snpdb,interval,ext = 10000)

`snpdb`	A GRange object or data frame, which is GWAS trait-associated SNPs downloaded from up-to-date dbGaP and NHGRI public database. It is maintained to be updated to the latest version. The data frame contains the following columns,`Trait`,`SNP`,`p.value`,`Chr`,`Position`,`Context`,`GENE_NAME`,`GENE_START`,`GENE_END`,`GENE_STRAND`. The data frame is in `data` subdirectory. Users are free to add more SNP records to the data frame for practical use.
`region`	A data frame, which is genomic intervals with three columns, chromosome, genomic start position, genomic end position.
`keyword`	The keyword is used when specific trait is of interest. If `keyword` is specified, only the SNPs associated to the trait are used for analyses. Otherwise, all traits will be analyzed.
`snpid`	SNP rs number
`gene`	Gene name
`pvalue`	SNPs with p-value less than this threshold are used for analyses.
`plot.type`	Either "densityplot" or "boxplot"
`ext`	Bp extended upstream and downstream
`xymax`	The maximum range on x-axis and y-axis
`interval`	A data frame, genomic interval:chromosome, genomic start position, genomic end position

`plotContext`	A pie plot with the distribution of SNP function class
`plotPvalue`	A density plot of -logPvalue of trait-associated SNPs
`plotSNP`	A plot of trait-associated SNP on chromosome
`plotGene`	A plot with the gene and possible nearby trait-associated SNPs
`plotInterval`	A plot with chromosome interval with possible nearby genes and trait-associated SNPs

Li Chen <li.chen@emory.edu>, Zhaohui Qin<zhaohui.qin@emory.edu>

	
	data(taSNP)
	plotContext(snpdb= taSNP,keyword="Autoimmune")
	plotGene(snpdb= taSNP,gene="ZFP92",ext=50000)
	plotSNP(snpdb= taSNP,snpid="rs766420",ext=50000)
	plotInterval(snpdb= taSNP,data.frame(chr="chrX",start=152633780,end=152737085))