getKEGGIDNName {AnnBuilder} | R Documentation |
These functions extract pathway and enzyme data from KEGG
ftp://ftp.genome.ad.jp/pub/kegg/pathways. The functions are used
by KEGG-class
.
getKEGGIDNName(object, exten = "/../map_title.tab") getKEGGOrgName(name) getLLPathMap(srcUrl, idNName, organism, fromWeb = TRUE) mapll2EC(id, srcUrl, organism, fromWeb, sep = "\t") parseEC(llNEC)
srcUrl |
srcUrl a character string for the url where
source data are available |
object |
object a KEGG object with the slots filled with
correct values |
exten |
exten a character string for data file name as an
extension |
name |
name a character string for the name of the
organism of concern. "human", "mouse", and "rat" are the valid
values for now |
organism |
organism same as name |
idNName |
idNName a named vector normally obtained obtained
by using function getKEGGIDNName |
sep |
sep a character string for the separators used to
separator entries in a file |
llNEC |
llNEC a line of tab separated character strings
with the first character string being a LocusLink id and second
being the mapping enzyme (EC) names |
id |
id a character string for the KEGG id used for
different pathway files |
fromWeb |
fromWeb a boolean to indicate whether a source
data file will be read from a web site or locally |
getKEGGIDNName
read the data file "map_title.tab" from
KEGG to obtain the mappings between KEGG ids and pathway
names.
getKEGGOrgName
takes the name for an organism and
returns a short verion of the name used by KEGG for that organism.
getLLPathMap
maps LocusLink ids to pathway and enzyme
names for an organism using various data files from KEGG.
mapll2EC
maps LocusLink ids to enzyme (EC) names for a
given pathway.
parseEC
extracts enzyme data from a line of tab
separated character strings to map a LocusLink id to enzyme (EC) names.
getKEGGIDNName
returns a named vector with KEGG ids
being the names and pathway names being values.
getKEGGOrgName
returns a character string.
getLLPathMap
returns a list of two elements named "llec"
and "llpathname". Each element is a matrix with mappings between
LocusLink ids to enzyme or pathway names.
mapll2EC
returns a matrix with the first column being
LocusLink ids and second enzyme (EC) names.
parseEC
returns two elements vector with the first
element being a LocusLink id and second being the mapping enzyme (EC)
names.
Jianhua Zhang
## Not run: getKEGGOrgName("Homo sapiens") # This group of code needs a while to finish # Url may change but was correct at the time of coding idNPath <- getKEGGIDNName(KEGG(organism = "Homo sapiens")) temp <- getLLPathMap("ftp://ftp.genome.ad.jp/pub/kegg/pathways", idNPath, "Homo sapiens") temp <- mapll2EC("00010", "ftp://ftp.genome.ad.jp/pub/kegg/pathways", "Homo sapiens", sep = "\t") ## End(Not run)