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Last data update: 2014.03.03

R: Retrieve trait-associated SNPs based

querys

R Documentation

Retrieve trait-associated SNPs based

Description

These are a group of functions to retrieve the trait-associated SNPs based on input

Usage

	
queryKeyword(snpdb, region=NULL, keyword = NULL, returnby = c("SNP_ID", "trait"), pvalue = 1e-3)

queryGene(snpdb, genes = NULL)

querySNP(snpdb, snpid, region = NULL)

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_ID`,`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
`genes`	Gene name
`pvalue`	SNPs with p-value less than this threshold are used for analyses.
`returnby`	Either SNP or trait. If `returnby` is specified as 'SNP_ID', a data frame based on 'SNP_ID' is returned. If `returnby` is specified as 'trait', a data frame based on 'trait' is returned.

Value

queryKeyword: Return a data frame of traits containing the keyword queryGene: Return a data frame of traits associated with the gene querySNP: Return a data frame of traits associated with the SNP

Author(s)

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

Examples

	
	data(taSNP)
	data(Tcell)
	x=queryKeyword(snpdb=taSNP,region=Tcell,keyword="Autoimmune",returnby="SNP_ID")
	x=queryGene(snpdb=taSNP,genes=c("AGRN","UBE2J2","SSU72"))
	x=querySNP(snpdb=taSNP,snpid=c("rs3766178","rs880051"))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(traseR)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/traseR/querys.Rd_%03d_medium.png", width=480, height=480)
> ### Name: querys
> ### Title: Retrieve trait-associated SNPs based
> ### Aliases: queryKeyword queryGene querySNP
> 
> ### ** Examples
> 
> 	
> 	data(taSNP)
> 	data(Tcell)
> 	x=queryKeyword(snpdb=taSNP,region=Tcell,keyword="Autoimmune",returnby="SNP_ID")
> 	x=queryGene(snpdb=taSNP,genes=c("AGRN","UBE2J2","SSU72"))
> 	x=querySNP(snpdb=taSNP,snpid=c("rs3766178","rs880051"))
> 	
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>