genemodel: create GRanges instance with model for a gene

In erma: epigenomic road map adventures

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")

erma documentation built on Nov. 8, 2020, 5:39 p.m.