Lung squamous cell carcinoma: CPTAC N-glycoproteome

Load the supplied JHU GENCODEv34 median-normalized glycoform-peptide abundance matrix as a glyexp::GlycoproteomicSE. Downloads are cached.

Usage

glyhub_CPTAC_LSCC(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Source

https://pdc.cancer.gov/pdc/cptac-pancancer Data use and attribution: https://pdc.cancer.gov/pdc/data-use-guidelines. The source data are not licensed under the package's MIT code license.

Arguments

kind: "curated" returns a data object; "raw" returns the path to a verified source archive. Raw archives are currently available for CPTAC.
cache_dir: Cache directory, defaulting to tools::R_user_dir("glyhub", "cache"). Set option glyhub.cache_dir to change the default.
refresh: Download the pinned resource again, even if cached.
offline: Prohibit downloads; require a verified local resource.

Details

The assay is 2^source_value, a linearized normalized abundance. Source log2 values, including zeros, are retained in metadata(x)$raw_abundance. Source None entries become NA; no filtering, imputation, aggregation or further normalization is performed. These data are an exception to the zero-to-NA convention used for GlycoPOST datasets.

Reference and QC columns remain present, with source-label-derived roles in colData. Unresolved roles remain unresolved. Repeated measurements are not independent patients. Intensity.Reference is retained in rowData(x)$intensity_reference_log2, not treated as a sample. Source peptide, gene and composition annotations are retained. N/H/F/S/G denotes HexNAc/Hex/Fuc/Neu5Ac/Neu5Gc. No structures are inferred. Protein accessions and absolute sites are unknown (NA); source gene annotations must not be treated as protein accessions.

Provenance records the supplied file hash and upstream checksum status. COAD and PDAC match upstream CRC and PDA after reversing column-prefix renaming; HGSC has not been matched to the supplied upstream MD5 list. The HGSC fractionation identity therefore remains unverified. See glyhub_catalog() for dimensions, sizes and download URLs.

Access