plots {traseR} | R Documentation

## Visualize of trait-associated SNPs

### Description

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

### Usage

    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)

### Arguments

`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

### Value

`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

### Author(s)

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

### Examples

    	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))

[Package traseR version 1.24.0 Index]