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List All Omes

ome_available_list.Rd

Return a character vector containing all available omes. These are the "full names" for each of the assays.

Usage

ome_available_list()

Value

A character vector containing all available omes.

Details

This vector is the vocabulary every accessor gates on: load_qc(), load_summary_stats() and load_differential_analysis() all resolve "all" through it and reject anything absent from it, so an ome missing here is an ome no accessor can return. It must therefore track what the pipeline actually builds, which is recorded in OME_TISSUE_CODE.

Two clinical omes are included as of v2.0. Clinical chemistry was a single "clinical-chemistry" assay in c1.3 and is now split into "metab-t-clinical" and "prot-clinical", each with its own QC, differential-analysis and summary-statistic objects.

"metab-meta-reg" was removed. It was dropped from the pipeline entirely, so no object was ever produced under that name and every accessor offered it as a choice that returned nothing.

The lab-* tiers in OME_TISSUE_CODE are deliberately absent. They are the raw clinical laboratory inputs, distributed as the cln_chemistry_* tables rather than as omes.

See also

metab_only_list(), tissue_available_list()

Examples

ome_available_list()
#>  [1] "prot-ol"              "prot-ph"              "prot-pr"             
#>  [4] "prot-clinical"        "transcript-rna-seq"   "epigen-methylcap-seq"
#>  [7] "epigen-atac-seq"      "metab-u-hilicpos"     "metab-u-ionpneg"     
#> [10] "metab-u-lrpneg"       "metab-u-lrppos"       "metab-u-rpneg"       
#> [13] "metab-u-rppos"        "metab-t-amines"       "metab-t-conv"        
#> [16] "metab-t-imm-crt"      "metab-t-oxylipneg"    "metab-t-tca"         
#> [19] "metab-t-nuc"          "metab-t-acoa"         "metab-t-ka"          
#> [22] "metab-t-clinical"