genemodForGviz {TFutils} | R Documentation

## create a GeneRegionTrack instance for selected symbols

### 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
    }

[Package TFutils version 1.4.0 Index]