Human organ atlas raw XIC matrix

Usage

glyhub_PXD070547_N_HumanAtlas(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Source

https://doi.org/10.1038/s41467-026-74631-7.

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.

Value

A glyexp::GlycoproteomicSE.

Details

57,884 source feature rows across 219 reported measurement columns.

Assay scale: Source Skyline extracted-ion chromatogram quantification; raw relative signal

Explicit source NA strings and blanks -> NA; no imputation, normalization, filtering, zero conversion or aggregation

Annotation joined only by exact ID: unmatched source rows retained with unknown molecular annotation

Source linkage notation retained, no unverified structure parser or inferred linkage

S monosaccharide is unspecified sialic acid; sialylated typed compositions remain NA

Source age/sex cells are cohort summaries, not person-level values; not propagated to samples

Use original measured columns, not the normalized or KNN/ComBat matrices

Measurement columns are not automatically independent biological samples. Source row identifiers, annotations and provenance are retained in metadata.

The assay preserves source numeric values. The metadata field raw_abundance means source numbers; it does not certify that the authors supplied unprocessed intensity.

Availability and source license

Downloaded from the existing data release through the verified cache. Source-license scope for the complete object remains unresolved; no new license is granted. See publication-decisions.tsv and object metadata for original sources and limitations.