search.glycans.by.name {KEGGSOAP} | R Documentation |
The functions provide access to KEGG LIGAND database http://www.genome.jp/kegg/ligand.html. Given a glycan name, a composition, a molecular weight, or a common sub-structure, one of the functions below can return a list of glycans identifiers from KEGG LIGAND database.
search.glycans.by.name(name) search.glycans.by.composition(composition) search.glycans.by.mass(mass, range) search.glycans.by.kcam(kcf, program, option, offset, limit)
name |
name a character string to indicate a glycan
name |
composition |
composition a character string to indicate
the composition of monosaccharides |
mass |
mass a float to indicate the mass computed from
the composition, excluding those in parentheses |
range |
range a float to indicate the range of molecular
weight when searching glycans by mass |
kcf |
kcf a character string to indicate the molecular
structure (carbohydrate sequence) of a glycan in KCF format |
program |
program a character string, either "gapped"
or "ungaped" |
option |
option a character string, either "global" or
"local" |
offset |
offset an integer |
limit |
limit an integer |
search.glycans.by.name
returns a list of glycans having the
specified name;
search.glycans.by.composition
returns a list
of glycans containing sugars indicated by the composition. Order
of the sugars (in parenthesis with number) is insensitive;
search.glycans.by.mass
returns a list of glycans having the
molecular weight around "mass" with some ambiguity (range);
search.glycans.by.subcomp
returns a list of glycans with
the alignment having common sub-structure calculated by the KCaM
program. You can obtain a KCF formatted structural data of matched
glycans using bget
with the "-f m" option to confirm the alignment.
All the functions return a character vector of glycan identifiers provided by KEGG LIGAND database
Nianhua Li
http://www.genome.jp/kegg/docs/keggapi_manual.html#label:105
if(require("SSOAP") && require("XML")){ glycans_1 <- search.glycans.by.name("Paragloboside") glycans_2 <- search.glycans.by.composition("(Man)4 (GalNAc)1") glycans_3 <- search.glycans.by.mass(689.6, 0.1) kcf <- bget("-f k gl:G12922") glycans_4 <- search.glycans.by.kcam(kcf, "gapped", "local", 1, 5) }