| sraGraph {SRAdb} | R Documentation |
This function will create a new graphNEL object from SRA accessions using function of entityGraph and SRA accessions are returned from SRA full text search using function of getSRA
sraGraph(search_terms, sra_con)
search_terms |
Free text search terms constructed according to SQLite query syntax defined here: http://www.sqlite.org/fts3.html#section_1_3 |
sra_con |
Connection to the SRAmetadb SQLite database |
This function is a wrapper of two functions: acc <- getSRA(search_terms, out_types='sra', sra_con, acc_only=TRUE)
and g <- entityGraph(acc). A graphNEL object with edgemode='directed' is created from input data.frame of SRA accessions and the plot function will draw a graph
A graphNEL object with edgemode='directed'
Jack Zhu <zhujack@mail.nih.gov> and Sean Davis <sdavis2@mail.nih.gov>
getSRA, sraConvert, entityGraph
if(file.exists('SRAmetadb.sqlite')) {
library(SRAdb)
library(Rgraphviz)
sra_dbname <- 'SRAmetadb.sqlite'
sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
## create a graphNEL object from SRA accessions, which are full text search results of terms 'primary thyroid cell line'
g <- sraGraph('primary thyroid cell line', sra_con)
attrs <- getDefaultAttrs(list(node=list(fillcolor='lightblue', shape='ellipse')))
plot(g, attrs=attrs)
## similiar search as the above, returned much larger data.frame and graph is too clouded
g <- sraGraph('Ewing Sarcoma', sra_con)
## Not run:
plot(g)
## End(Not run)
} else {
print("use getSRAdbFile() to get a copy of the SRAmetadb.sqlite file
and then rerun the example")
}