snpsNear {GGBase} | R Documentation

## obtain list of rs numbers for snps near a gene

### Description

obtain list of rs numbers for snps near a gene

### Usage

    snpsNear(sym, radius=1e+05, chrnum, ...)

### Arguments

`sym` | instance of genesym class [e.g., use genesym(string) for gene 'string'], or of rsid class, or of numeric class. An instance of `GSEABase-class` can also be supplied if it has `geneIdType` AnnotationIdentifier.
`radius` | number of base-pairs in each direction to look
`chrnum` | chrnum instance .. optional
`...` | options not now in use

### Details

simple arithmetic based on output of snpLocs.Hs

### Value

character vector of rsxxxxxx, dbSNP id, according to locations from SNPlocs.Hsapiens.dbSNP.20071016 package, as transferred to snpLocs.Hs resource in GGBase
note that an attribute 'target' is returned, a named vector with components chr and loc describing chromosome and location of the target for which nearby SNPs are sought

### Note

first invocation can take longer than subsequent, if snpLocs.Hs has not been invoked previously

### Author(s)

Vince Carey <stvjc@channing.harvard.edu>

### Examples

    nearc = snpsNear(genesym("CPNE1"), 10000, chrnum(20))
    library(GGtools)
    data(hmceuB36.2021)
    ss = smList(hmceuB36.2021)[[1]]
    # following calculation requires new "[" for j an instance of rsid
    clo = ss[ , rsid(snpsNear(rsid("rs6060535"), rad=1500, chrnum(20))) ]
    clo
    # try a gene set
    library(GSEABase)
    s1 = GeneSet(c("CPNE1", "ADA"), geneIdType=SymbolIdentifier())
    s2 = s1
    geneIdType(s2) = AnnotationIdentifier("illuminaHumanv1.db")
    s2
    sapply(snpsNear(s2), length)

[Package GGBase version 3.4.0 Index]