Mouse brain Glyco-Decipher chromatographic areas

Usage

glyhub_IPX0011099000_N_Brain(
  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/s41467-025-60437-6.

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

20,191 source feature rows across 60 reported measurement columns.

Assay scale: Source untransformed chromatographic Area

Feature grain: Peptide / glycan / source sites / compensation voltage

Source selection: Raw Area exports preferred over Supplementary Data6 processed matrix

No normalization, log transform, imputation, filtering, aggregation or zero conversion

Exact source identity union; a row absent from a run becomes structural NA; reported zero remains zero

Separate FAIMS compensation voltages retained as separate features

Unambiguous single accession@position parsed; multiple site assignments retained verbatim with canonical NA

Run code and region code retained without guessing disease, age, or anatomical mapping

Source extraction and identification filtering precede these exports; unspecified extraction 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.