col_data_with_genes: Sample Variables with Selected Gene Information

In insightsengineering/hermes: Preprocessing, analyzing, and reporting of RNA-seq data

Sample Variables with Selected Gene Information

Description

This obtains the sample variables of a HermesData object together with selected gene information.

Usage

col_data_with_genes(object, assay_name, genes)

Arguments

object	(AnyHermesData) input experiment.
assay_name	(string) which assay to use.
genes	(GeneSpec) which genes or which gene signature should be extracted.

Value

The combined data set, where the additional attribute gene_cols contains the names of the columns obtained by extracting the genes information.

Note

The class of the returned data set will depend on the class of colData, so usually will be S4Vectors::DFrame.

Examples

result <- col_data_with_genes(hermes_data, "counts", gene_spec("GeneID:1820"))
tail(names(result))
result$GeneID.1820

insightsengineering/hermes documentation built on Sept. 19, 2024, 9:06 p.m.