querys: Retrieve trait-associated SNPs based

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

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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 <[email protected]>, Zhaohui Qin<[email protected]>

Examples

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	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"))
	

traseR documentation built on Oct. 31, 2019, 2:10 a.m.