HCC discovery cohort selected processed features

Usage

glyhub_PXD065283_N_DiscoverySelected(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Source

https://doi.org/10.1002/advs.202516299.

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

1,038 source feature rows across 140 reported measurement columns.

Assay scale: Source median-normalized, log2-transformed, normally imputed abundance; DE-selected features

Source selection: Only verified public individual clinical matrix; earliest unnormalized clinical table unavailable through inspected sources. QC linear table is a different experiment, not a substitute for clinical samples.

All source cells preserved; no new normalization, imputation, filtering, inverse transform or aggregation

Source workflow: MBR, source missingness filtering, median normalization, log2, normal-distribution interpolation, then differential-feature selection (p<=0.01 and absolute log2FC>=1)

1038 selected features and 140 discovery samples; not the full 8902-feature matrix or 60-person validation cohort. Feature selection uses case labels; unsuitable for unbiased discovery or classifier performance estimates.

No exponentiation to claim recovered original intensity; unspecified upstream settings remain unknown

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.