sraGraph: Create a new graphNEL object of SRA accessios from SRA full...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/sraGraph.R

Description

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

Usage

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sraGraph(search_terms, sra_con)

Arguments

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

Details

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

Value

A graphNEL object with edgemode='directed'

Author(s)

Jack Zhu <[email protected]> and Sean Davis <[email protected]>

See Also

getSRA, sraConvert, entityGraph

Examples

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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")
}

seandavi/SRAdb documentation built on Feb. 21, 2018, 5:21 a.m.