entityGraph: Create a new graphNEL object from an input entity matrix or...

In zhujack/SRAdb: A compilation of metadata from NCBI SRA and tools

Create a new graphNEL object from an input entity matrix or data.frame

Description

This function will create a new graphNEL object from an input entity matrix or data.frame

Usage

entityGraph(df)

Arguments

df	A matrix or data.frame

Details

A graphNEL object with edgemode='directed' is created from input data.frame and the plot function will draw a graph

Value

A graphNEL object with edgemode='directed'

Author(s)

Jack Zhu <[e-mail]> and Sean Davis <[e-mail]>

See Also

getSRA, sraConvert, sraGraph

Examples

## Using the SRAmetadb demo database

	library(SRAdb)
	sra_dbname <- file.path(system.file('extdata', package='SRAdb'), 'SRAmetadb_demo.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'
  	acc <- getSRA (search_terms ='MCF7 OR "MCF-7"', out_types=c('sra'), sra_con=sra_con, acc_only=TRUE) 
  	g <- entityGraph(acc)
  	## Not run: 
  	library(Rgraphviz)
  	attrs <- getDefaultAttrs(list(node=list(fillcolor='lightblue', shape='ellipse')))
  	plot(g, attrs= attrs)
  	
## End(Not run)

## The actual SRAmetadb sqlite database can be downloaded using function: getSRAdbFile. Warning: the actual SRAmetadb sqlite database is pretty large (> 35GB as of May, 2018) after uncompression. So, downloading and uncompressing of the actual SRAmetadb sqlite could take quite a few minutes depending on your network bandwidth. Direct links for downloading the SRAmetadb sqlite database:  https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz

zhujack/SRAdb documentation built on Dec. 6, 2024, 2:15 a.m.