gQTLseq (version 0.0.10)

genemap: generate a GRanges from an annotation resource that addresses gene locations

Description

generate a GRanges from an annotation resource that addresses gene locations

Usage

genemap(orgref, genes = NULL, 
  geneannotype, chrsToUse = as.character(1:22), 
  na.action = na.omit, forceUCSC = TRUE, 
  addCHRLENGTHS = TRUE, trim = TRUE)

Arguments

orgref

instance of OrganismDb or ChipDb

genes

vector of tokens to be mapped; if NULL, all tokens in keys(orgref, keytype=geneannotype) are used

geneannotype

character, an element of keytypes(orgref)

chrsToUse

vector identifying tokens with acceptable values for the ranges of CHRLOC and CHRLOCEND columns of the annotation resource

na.action

an interim result of the annotation query is a data.frame instance; na.action will be applied to this data.frame prior to GRanges construction

forceUCSC

logical: if UCSC chromosome identifiers are not employed and forceUCSC is TRUE, ``chr'' will be prepended to chromosome numbers.

addCHRLENGTHS

logical, should action be taken to add CHRLENGTH information to the seqinfo for the output

trim

logical, if TRUE, the trim method will be applied before returning to ensure all ranges are consistent with CHRLENGTHs

Value

• GRanges instance

Examples

if (require(Homo.sapiens)) {
 gm = genemap(Homo.sapiens, geneannotype="ENTREZID")
 gm
 }
# also consider
# genemap(Homo.sapiens, geneannotype="ENSEMBL")
# and check relationship to rowRanges(montpick.summ) -- there are
# minor discrepancies in ranges