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]