Rat serum N-glycans after chronic herbicide exposure

Serum N-glycan profiles from control and glyphosate-based-herbicide-exposed rats, comprising six control males, six control females, five exposed males and seven exposed females.

Usage

glyhub_GPST000403_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 113 features and 24 observations. The abundance assay is in relative abundance (%). rowData has no glycan_structure column because no feature has a supported structural annotation.

Source

GlycoPOST GPST000403. Sheet1. Study: https://doi.org/10.3390/biom14091077. Repository: https://glycopost.glycosmos.org/entry/GPST000403.

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

The 113-feature matrix is the final percentage matrix on Sheet 1, corroborated by published Supplementary Tables S1 and S2. Sheet 2 contains a differently normalised intermediate for the same samples and is not duplicated as independent observations. Five-digit glycan codes follow the paper order HexNAc, Hex, Fuc, NeuAc and NeuGc. Compositions are retained; structural isomers are unresolved.

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_GPST000403_N") to load this dataset.