genemodelDF: use EnsDb to generate an exon-level model of genes identified...

In shwetagopaul92/TFutils: TFutils

Description

use EnsDb to generate an exon-level model of genes identified by symbol

Usage

genemodelDF(sym, resource, columnsKept = c("gene_id", "tx_id"), ...)

Arguments

sym	a character() vector of gene symbols
resource	should be or inherit from EnsDb, answering exons(), with AnnotationFilter::SymbolFilter as filter parameter
columnsKept	character vector used as columns param in exons()
...	passed to exons()

Value

data.frame instance with exons in rows

Note

There are many approaches available to acquiring 'gene models' in Bioconductor; this one emphasizes the use of the exons method for Ensembl annotation.

Examples

if (requireNamespace("EnsDb.Hsapiens.v75")) {
 orm = genemodelDF("ORMDL3", EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75)
 dim(orm)
}
head(orm)

shwetagopaul92/TFutils documentation built on May 26, 2019, 4:32 a.m.