pGlycoQuant HCC cell-line source intensities

Usage

glyhub_MSV000089484_N_HCC(
  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/s41467-022-35172-x.

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

11,001 source feature rows across 12 reported measurement columns.

Assay scale: Source SILAC glycoform-site intensity; -1 mapped to NA by user-confirmed curation convention

Exactly 40338 source -1 entries mapped to assay NA by explicit user instruction; the author has not directly defined this code in inspected sources

Original -1 entries and every source value remain in metadata raw_abundance

All 2137 zeros and every positive intensity preserved exactly; no log transform, normalization, imputation or filtering

One record per source protein/site/glycan row; no invented peptide sequence or PSM

The 6435-row filtered sheet is not a separate dataset or cohort

Repeat labels do not establish independent biological replication

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

The assay maps source -1 to NA by user-confirmed convention, not an author-confirmed definition. All source values, including -1, remain in metadata raw_abundance; zeros and positive values are unchanged.

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.