querys {traseR} | R Documentation |
These are a group of functions to retrieve the trait-associated SNPs based on input
queryKeyword(snpdb, region=NULL, keyword = NULL, returnby = c("SNP_ID", "trait"), pvalue = 1e-3) queryGene(snpdb, genes = NULL) querySNP(snpdb, snpid, region = NULL)
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, |
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 |
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 |
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
Li Chen <li.chen@emory.edu>, Zhaohui Qin<zhaohui.qin@emory.edu>
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"))