Bladder-tissue N-glycans across cancer stages

N-glycan profiles from healthy bladder, cystitis and Ta, T1 and muscle-invasive bladder tumours. The table contains five observations in each of the first four groups and eight in the muscle-invasive group.

Usage

glyhub_GPST000585_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 23 features and 28 observations. The abundance assay is in source-labelled relative abundance (%). rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000585. Table S1. Study: https://doi.org/10.3390/ijms26104891. Repository: https://glycopost.glycosmos.org/entry/GPST000585.

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

PNGase F-released, reduced and permethylated N-glycans were quantified by mass spectrometry. Source Table S1 relative-abundance values are preserved without rescaling; paired peak areas are retained in row annotations rather than duplicating the dataset. n.d. cells are missing. Composition identities and source glycan classes are preserved without converting class labels into asserted structures.

Source-derived composition annotations; linkage information is retained as source annotation without inferring a full topology. No complete unambiguous structures are asserted.

Access

Use glyhub_load("glyhub_GPST000585_N") to load this dataset.