getCisMap: create, using Bioconductor annotation resources, a structure...

In GGtools: software and data for analyses in genetics of gene expression

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

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.

Value

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

Examples

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

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.