Loads internal datasets from the IOBR package. Supports both sysdata (internal) and exported data files included in the package.
Arguments
- name
Character string. Name of the dataset to load. Must be a single value. Available datasets include: - Expression data: `"eset_stad"`, `"imvigor210_eset"`, `"melanoma_data"` - Signatures: `"signature_tme"`, `"signature_metabolism"`, `"signature_collection"` - Gene sets: `"hallmark"`, `"kegg"`, `"go_bp"`, `"go_cc"`, `"go_mf"` - Cell markers: `"cellmarkers"`, `"mcp_genes"` - Phenotype data: `"pdata_stad"`, `"pdata_sig_tme"`, `"pdata_acrg"` - Reference data: `"xCell.data"`, `"quantiseq_data"`, `"TRef"`, `"BRef"` - Color palettes: `"palette1"`, `"palette2"`, `"palette3"`, `"palette4"`
Value
Dataset object, typically a `list`, `data.frame`, or `matrix`. The exact type depends on the requested dataset.
Examples
# Load signature collection
sig_tme <- load_data("signature_tme")
# Load expression data
eset <- load_data("eset_stad")
# Load color palette
colors <- load_data("palette1")
# Error handling with suggestions for similar names
try(load_data("sign_tme")) # Will suggest "signature_tme"
#> Error in load_data("sign_tme") :
#> Dataset "sign_tme" not found in IOBR package.
#> ℹ Available datasets: BRef, PurityDataAffy, SI_geneset, TRef, anno_gc_vm32,
#> anno_grch38, anno_hug133plus2, anno_illumina, anno_rnaseq, cancer_type_genes,
#> cellmarkers, common_genes, deg, eset_blca, eset_gse62254, eset_stad,
#> eset_tme_stad, go_bp, go_cc, go_mf, hallmark, immuneCuratedData,
#> imvigor210_eset, imvigor210_pdata, imvigor210_sig, ips_gene_set, kegg,
#> length_ensembl, lm22, mRNA_cell_default, mcp_genes, mcp_probesets,
#> melanoma_data, msig_immune, msig_sc, mus_human_gene_symbol, null_models,
#> onco_sig, palette1, palette2, palette3, palette4, panel_for_gene,
#> panel_for_signature, patterns_to_na, pdata_GSE63557, pdata_acrg,
#> pdata_sig_tme, pdata_sig_tme_binary, pdata_stad ...