get.genes.by.motifs {KEGGSOAP} | R Documentation |
Given a set of motif ids, the function searches the databases implied by the motif ids for genes containing the motifs represneted by the motif ids
get.genes.by.motifs(motif.id.list, start, max.results)
motif.id.list |
motif.id.list a vector of character strings
for the ids of the motifs that are conserved by genes across
organisms |
start |
start an integer to indicate the location of the
entry in the query results from which the results will be
extracted and returned |
max.results |
max.results an integer to indicate the
maximum number of entries that will be extracted from the query
results and returned |
KEGG seems to have two ways of defining the ids for motifs. One is the
motif ids obtained through get.motifs.by.gene
, where
pfam, tfam, pspt, pspf are used for the Pfam, TIGRFAM, PROSITE
pattern, and PROSITE profile database, respectively and for the first
part of a motif id (e. g. pfam:aakinase). Another is the motif ids
used to query the databases for genes that contain the motif, where
only the first two letters of the abbreviations for databases form the
first part of a motif id (e. g. pf:aakinase)
The function returns a named vector with the names of the vector being the textual definition of genes and values of the vector being the ids used by KEGG to represent genes
Jianhua Zhang
http://www.genome.jp/kegg/soap/doc/keggapi_manual.html
if(require("SSOAP") && require("XML")){ genes <- get.genes.by.motifs(c("pf:DnaJ", "ps:DNAJ_2"), 1, 10) }