Sample Variables with Selected Gene Information

Source: R/join_cdisc.R

[Experimental]

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

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))
#> [1] "COHORT"            "TTYPE"             "STDSSDY"          
#> [4] "low_depth_flag"    "tech_failure_flag" "GeneID.1820"      
result$GeneID.1820
#>  [1]  49 153  94  54 111 567 118 171 180  16 386  57 242  73 362 144 124 243  79
#> [20] 161