Helper Function to Format Gene Choices — h_gene

Given a hermes::AnyHermesData data object, as well as the annotation column name to use as gene name, this function formats the contained genes as a data.frame ready for consumption in h_order_genes() e.g.

Usage

h_gene_data(object, name_annotation)

Arguments

object: (AnyHermesData)
contains RNA-seq values for one experiment.
name_annotation: (string or NULL)
which annotation column to use as name to return in the genes data. If NULL, then the name column will be set to empty strings.

Value

A data.frame with id and name columns containing all genes from object.

Details

Note that missing names or names that only contain whitespace are replaced by empty strings for consistency and better labeling in the UI downstream

Examples

object <- hermes::hermes_data[1:10, ]
h_gene_data(object, "symbol")
#>                  id         name
#> 1      GeneID:11185         INMT
#> 2      GeneID:10677         AVIL
#> 3  GeneID:101928428 LOC101928428
#> 4  GeneID:100422835      MIR3183
#> 5  GeneID:102466731     MIR6769A
#> 6      GeneID:64881       PCDH20
#> 7     GeneID:286205         SCAI
#> 8       GeneID:8365     HIST1H4H
#> 9       GeneID:6804        STX1A
#> 10 GeneID:100423018    MIR3156-3