genemodel {erma}R Documentation

create GRanges instance with model for a gene

Description

create GRanges instance with model for a gene

Usage

genemodel(key, keytype, annoResource = Homo.sapiens,
   keepStandardChromosomes=TRUE)
geneTxRange(sym, annoResource = Homo.sapiens)
map2range(maptag="17q12", annoResource = Homo.sapiens)

Arguments

sym

symbol used as key into annoResource with keytype SYMBOL

key

string used as key into annoResource with keytype keytype

maptag

string used as key into annoResource with keytype MAP

keytype

string used as keytype for select with annoResource

annoResource

OrganismDb instance; genemodel will also work with an EnsDb instance

keepStandardChromosomes

if true, will eliminate non-standard chromosomes using the eponymous function from GenomeInfoDb, with pruning.mode = 'coarse'

Details

map2range will obtain all TXSTART and TXEND for genes identified through select with key maptag and return a single range with min TXSTART and max TXEND

Value

a GRanges instance

Note

genemodel revised Aug 10 2015. Direct operations on Homo.sapiens, much faster. geneTxRange added Aug 10 2015.

Examples

genemodel("IL33")
geneTxRange("IL33")
map2range("17q12")

[Package erma version 1.3.0 Index]