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 "HMO", "N", "GSL", "GAG", "O", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", "O-Glc", or "GPI". When "O", all O-linked glycans are included. Specific O-glycan types only include that subtype. 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.

The confidence attribute is preserved by vector operations that subset, reorder, repeat, combine, or replace glycans. When vectors containing the same glycan with different confidence values are combined, the maximum confidence is used for every occurrence of that glycan.

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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GlyGen Glycan Data

Description

A curated dataset glycan structures from GlyGen Data v2.12.1, with 49,728 glycan structures currently available.

Usage

glydb_data

Format

A tibble with 49,728 rows and 6 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, such as "HMO", "N", "GSL", "GAG", "O", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", "O-Glc", or "GPI".

• confidence: Confidence score used to rank glycans.

Source

https://data.glygen.org/ln2data/releases/data/v-2.12.1/reviewed/

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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,
  mono_type = "concrete"
)

Arguments

structure_level	Either "intact" or "topological". 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 "HMO", "N", "GSL", "GAG", "O", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", "O-Glc", or "GPI". When "O", all O-linked glycans are included. Specific O-glycan types only include that subtype. 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.
mono_type	Either "generic" or "concrete". Default is "concrete". See glyrepr::get_mono_type() for details.

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.

The confidence attribute is preserved by vector operations that subset, reorder, repeat, combine, or replace glycans. When vectors containing the same glycan with different confidence values are combined, the maximum confidence is used for every occurrence of that glycan.

Examples

glydb_structures()
glydb_structures(structure_level = "topological")
glydb_structures(mono_type = "generic")
glydb_structures(structure_level = "topological", mono_type = "generic")
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

Look up GlyTouCan accessions in the bundled glydb_data.

Usage

glytoucan_to_struc(glytoucan_ac)

Arguments

glytoucan_ac

A character vector of GlyTouCan accessions.

Value

A glyrepr::glycan_structure() vector. Accessions without a bundled match are returned as NA values in their original positions, and a warning is emitted.

Examples

glytoucan_to_struc("G17689DH")

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Convert Glycan Structures to GlyTouCan Accessions

Description

Match glycan structures to accessions in the bundled glydb_data.

Usage

struc_to_glytoucan(strucs)

Arguments

strucs

A glyrepr::glycan_structure() vector or a character vector of IUPAC-condensed glycan structures.

Details

Missing anomeric positions are filled with glyrepr::fill_anomer_pos() in both the input and bundled structures before matching. When multiple bundled rows normalize to the same structure, the accession from the first row is returned.

Value

A character vector of GlyTouCan accessions. Structures without a bundled match are returned as NA values in their original positions, and a warning is emitted.

Examples

struc_to_glytoucan(glydb_data$glycan_structure[1])

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