getAreaFromGeneNames {AllelicImbalance} | R Documentation |
Given a character vector with genesymbols and an OrgDb object, this function returns a GRanges giving the coordinates of the genes.
getAreaFromGeneNames(genesymbols, ...) ## S4 method for signature 'character' getAreaFromGeneNames(genesymbols, OrgDb, leftFlank = 0, rightFlank = 0, na.rm = FALSE, verbose = TRUE)
genesymbols |
A character vector that contains genesymbols of genes from which we wish to retrieve the coordinates |
... |
arguments to pass on |
OrgDb |
An |
leftFlank |
A |
rightFlank |
A |
na.rm |
A |
verbose |
Setting |
This function is a convenience function that can be used to determine which
genomic coordinates to specify to e.g. impBamGAL
when retrieving
reads.
The function cannot handle genes that do not exist in the annotation. To remove these please set the na.rm=TRUE.
getAreaFromGeneNames
returns a GRanges object with genomic
coordinates around the specified genes
Jesper R. Gadin, Lasse Folkersen
#load example data data(ASEset) #get counts at the three positions specified in GRvariants library(org.Hs.eg.db ) searchArea<-getAreaFromGeneNames(c('PAX8','TLR7'), org.Hs.eg.db)