Package 'glydb'

Get Compositions From Glydb Data

Description

Get unique glycan compositions from glydb_data as a glyrepr::glycan_composition() vector.

Usage

glydb_compositions(
  mono_type = "concrete",
  species = NULL,
  glycan_type = NULL,
  mono_range = NULL
)

Arguments

mono_type	Either "generic" or "concrete". Default is "concrete". See glyrepr::get_mono_type() for details.
species	A string of specie names. See glydb_species() for available specie names. Default is NULL, which means glycans from all species are included.
glycan_type	A string of glycan types. Can be "N", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", "O-Glc". Default is NULL, which means glycans of all types are included.
mono_range	A named list for filtering compositions by monosaccharide counts. Each element should be an integer vector of length 2 specifying the minimum and maximum count for that monosaccharide. Monosaccharides not specified will be excluded (count = 0). Use NULL for no filtering. See examples for usage.

Value

A glyrepr::glycan_composition() vector, with a confidence attribute as a numeric vector with the same length.

Confidence

The returned value has a confidence attribute: a numeric vector of the same length as the result containing log-transformed citation counts for each glycan in glydb_data. When multiple glycans are aggregated into lower-resolution structures or compositions, the maximum confidence score is retained.

Note that the confidence attribute will be lost after any vector operation like subsetting. Therefore, if used with glyanno, the returned value should not be modified manually.

Examples

glydb_compositions()
glydb_compositions(mono_type = "generic")
glydb_compositions(species = "Homo sapiens")
glydb_compositions(glycan_type = "N")
glydb_compositions(glycan_type = "N", mono_range = list(Hex = c(5L, 10L)))
glydb_compositions(mono_range = list(Hex = c(3L, 9L), HexNAc = c(2L, 6L)))

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Fully Determined GlyTouCan Glycan Data

Description

A curated dataset of fully determined glycans from GlyTouCan. "Fully determined" means that all linkages, substituents, anomers, and monosaccharides are fully specified. The dataset is derived from the GlyTouCan v2.11.1 release, with 7,125 glycan structures currently available.

Usage

glydb_data

Format

A tibble with 7,125 rows and 5 variables:

• glytoucan_ac: GlyTouCan accession.

• glycan_structure: Glycan structure (glyrepr::glycan_structure()).

• glycan_composition: Glycan composition (glyrepr::glycan_composition()).

• species: Specie names, separated by semicolons. Unknown species are NAs.

• glycan_type: Glycan type, one of "N", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", "O-Glc".

Source

https://data.glygen.org

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Get Supported Species From Glydb Data

Description

Get a character vector of supported species from glydb_data.

Usage

glydb_species()

Value

A character vector of supported species.

Examples

glydb_species()

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Get Structures From Glydb Data

Description

Get unique glycan structures from glydb_data as a glyrepr::glycan_structure() vector.

Usage

glydb_structures(
  structure_level = "intact",
  species = NULL,
  glycan_type = NULL,
  mono_range = NULL
)

Arguments

structure_level	Either "intact", "topological", or "basic". Default is "intact". See glyrepr::get_structure_level() for details.
species	A string of specie names. See glydb_species() for available specie names. Default is NULL, which means glycans from all species are included.
glycan_type	A string of glycan types. Can be "N", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", "O-Glc". Default is NULL, which means glycans of all types are included.
mono_range	A named list for filtering structures by monosaccharide counts. Each element should be an integer vector of length 2 specifying the minimum and maximum count for that monosaccharide. Monosaccharides not specified will be excluded (count = 0). Use NULL for no filtering. See examples for usage.

Value

A glyrepr::glycan_structure() vector, with a confidence attribute as a numeric vector with the same length.

Confidence

The returned value has a confidence attribute: a numeric vector of the same length as the result containing log-transformed citation counts for each glycan in glydb_data. When multiple glycans are aggregated into lower-resolution structures or compositions, the maximum confidence score is retained.

Note that the confidence attribute will be lost after any vector operation like subsetting. Therefore, if used with glyanno, the returned value should not be modified manually.

Examples

glydb_structures()
glydb_structures(structure_level = "topological")
glydb_structures(structure_level = "basic")
glydb_structures(species = "Homo sapiens")
glydb_structures(glycan_type = "N")
glydb_structures(glycan_type = "N", mono_range = list(Hex = c(5L, 10L)))
glydb_structures(mono_range = list(Hex = c(3L, 9L), HexNAc = c(2L, 6L)))

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Convert GlyTouCan Accessions to Glycan Structures

Description

Fetch GlyTouCan accessions from the GlyGen API and parse the returned IUPAC strings as glyrepr::glycan_structure() values.

Usage

glytoucan_to_struc(glytoucan_ac)

Arguments

glytoucan_ac

A character vector of GlyTouCan accessions.

Value

A glyrepr::glycan_structure() vector. Accessions that cannot be fetched or parsed are returned as NA values in their original positions, and a warning is emitted.

Examples

glytoucan_to_struc("G17689DH")

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