GGtools (version 5.8.0)

getCisMap: create, using Bioconductor annotation resources, a structure that enumerates SNP in the vicinity of ('cis' to) genes

Description

create a structure that enumerates SNP in the vicinity of ('cis' to) genes

Usage

getCisMap(radius = 50000, gchr = "20",  schr = "ch20", geneannopk = "illuminaHumanv1.db",  snpannopk = snplocsDefault(), as.GRangesList = FALSE, excludeRadius=NULL)

Arguments

radius

How far, in bases, up or down stream from the asserted coding region limits to include SNP

gchr

the token to be used to acquire locations for probes on a specified chromosome, using revmap([dbpk]CHR)

schr

the token to be used to acquire locations for SNP on a specified chromosome, using snplocs

geneannopk

character string naming a Bioconductor .db expression chip annotation package; or a complex string with first part naming a Bioconductor FDb.* annotation package, colon separator, and a second string naming the getter hook that when called returns a GRanges with names corresponding to features and ranges corresponding to feature extents. For example "FDb.InfiniumMethylation.hg19:get27k" is valid. Note that in this case, gchr must have prefix "chr".

snpannopk

character string naming a Bioconductor SNPlocs.* SNP metadata package

as.GRangesList

logical telling whether a GRangesList should be returned

excludeRadius

numeric or NULL: radius of interval around gene extent from which SNP will be excluded, required to be less than radius

Value

Instance of cisMap class, which will retain SNP location, gene range, and radius information for auditing.

Details

This is a utility that the developer would rather not export. The complexity of harmonizing queries among probe and SNP annotation resources leads to a somewhat fragile product. Users who have their own gene ranges and SNP locations can examine the namelist component of the output of the default call to see what is expected for the *.cis.eQTLs function. For the set of chromosomes to be analyzed, there will be a list of chromosome specific namelist-like lists.

Examples

 ## Not run: 
#   getCisMap()
#  ## End(Not run)