genemodForGviz: create a GeneRegionTrack instance for selected symbols

In vjcitn/TFutils: TFutils

Description

create a GeneRegionTrack instance for selected symbols

Usage

genemodForGviz(
  sym = "ORMDL3",
  id_elem = c("symbol", "tx_id"),
  resource = EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75,
  ...
)

Arguments

sym	character vector of gene symbols, should be neighboring genes
id_elem	vector of names of columns generated by genemodelDF to be used to label transcripts
resource	should be or inherit from EnsDb, answering exons(), with AnnotationFilter::SymbolFilter as filter parameter
...	passed to genemodelDF

Value

instance of Gviz GeneRegionTrack

Note

This function helps to display the locations of TF binding sites in the context of complex gene models. A complication is that we have nice visualization of quantitative affinity predictions for TFs in the vignette, based on ggplot2, but it is not clear how to use that specific code to work with Gviz.

Examples

if (requireNamespace("EnsDb.Hsapiens.v75") &
    requireNamespace("Gviz")) {
 orm = genemodForGviz("ORMDL3", resource= EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75)
 orm
 Gviz::plotTracks(orm, showId=TRUE) # change id_elem for shorter id string
}

vjcitn/TFutils documentation built on Oct. 25, 2021, 3:01 p.m.