StringDB PPI grabber

string.R

# Libraries
# ------------------------------------------------------------------------------
library("RCurl")
library("bitops")


# Define functions
# ------------------------------------------------------------------------------
getInteractions = function(id,score,limit,species=9606,print=FALSE){

	# --------------------------------------------------------------------
	# Param    Example         Description
	# --------------------------------------------------------------------
	# id       id="PLCG1"      The id to search the stringdb for
	# score    score=800       800/1000 = 80% chance of interaction
	# limit    limit=10        Only include the top 10 interactions
	# species  species=9606    The species, 9606 is human
	# print    print=TRUE      Print the browser pastable link to stringdb
	# --------------------------------------------------------------------

	# Check parameters
	if( length(id) != 1 ){ stop("getInteractions error: 'id' must have length 1!") }
	if( !is.numeric(score) & 0 <= score & score <= 999 ){ stop("getInteractions error: 'score' must be numeric between 0 and 999!") }
	if( !is.numeric(limit) ){ stop("getInteractions error: 'limit' must be numeric!") }
	if( !is.numeric(species) ){ stop("getInteractions error: 'species' must be numeric!") }
	if( !is.logical(print) ){ stop("getInteractions error: 'print' must be logical!") }

	# Create API request
	stringdb = "http://string-db.org/api/psi-mi-tab/interactions?"
	request  = paste0("identifier=",id,"&required_score=",score,"&limit=",limit,"&species=",species)
	url      = paste0(stringdb,request)
	if( print ){ cat(url,"\n") }

	# Retrieve request and check if 'id' is recognised by stringdb
	text = getURL(url)
	if( print ){ print(text) }
	if( text == "\n" | grepl('ERROR_NOT_FOUND',text) ){ return(NA) }

	# Read and parse results
	results = read.table(textConnection(text),stringsAsFactors=FALSE)
	results = subset(results,subset=(V3==id | V4==id))
	match   = regexpr("[[:digit:]].[[:digit:]]+", results$V15)
	scores  = as.numeric(regmatches(results$V15, match))
	output  = cbind(results$V3,results$V4,scores)
	output  = as.data.frame(t(apply(output,1,function(x){ return(x[-which(x==id)]) })))
	colnames(output) = c("PPI","SCORE")
	return(output)

}