Serum N-glycan profiles across hepatocellular carcinoma progression

MALDI-TOF serum N-glycomics from the hepatocellular carcinoma study, retaining the complete published pre-processing abundance table.

Usage

glyhub_GPST000584_N(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Format

A glyexp::GlycomicSE with 201 features and 743 observations. The abundance assay is in peak area. rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000584. raw. Study: https://doi.org/10.1038/s41467-026-68579-x. Repository: https://glycopost.glycosmos.org/entry/GPST000584.

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 raw sheet of Supplementary Data 2 contains 201 composition features and 743 source observations. The separate processed sheet is a filtered, normalized subset and is not appended as independent samples. Published clinical fields from Supplementary Data 8 are joined by exact sample ID; unmatched samples retain missing clinical metadata. The assay contains original peak-area measurements, with source zeros represented as missing and no new imputation or normalization. Composition-level measurements do not establish glycan topology or linkage isomers. Disease groups are joined from explicit sample/group columns in the source-data workbook, without inferring groups from sample numbering.

Source molecular compositions retained without inferring glycosidic linkages.

Access

Use glyhub_load("glyhub_GPST000584_N") to load this dataset.