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

Description Usage Arguments Value Note Examples

View source: R/genemodel2.R

Description

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

Usage

1
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

1
2
3
4
5
if (requireNamespace("EnsDb.Hsapiens.v75")) {
 orm = genemodelDF("ORMDL3", EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75)
 dim(orm)
}
head(orm)

TFutils documentation built on May 2, 2020, 2:01 a.m.