Visualize of trait-associated SNPs

Share:

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
	
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

1
2
3
4
5
6
	
	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))