R/utils.R

Defines functions content2df prideMiniList2DF prideAllList2DF

content2df <- function(content.pride){
	df.pride <- data.frame(accession= content.pride$accession,
	species = pleural2single(content.pride$species),
	tissues = pleural2single(content.pride$tissues),
	title = content.pride$title,
	otherOmicsLink = content.pride$otherOmicsLink,
	numProteins = content.pride$numProteins,
	numPeptides = content.pride$numPeptides,
	numSpectra = content.pride$numSpectra,
	numUniquePeptides = content.pride$numUniquePeptides,
	numIdentifiedSpectra = content.pride$numIdentifiedSpectra,
	postTranslationalModNames = pleural2single(content.pride$ptmNames),
	#------
	publicationDate = content.pride$publicationDate,
	submissionType = content.pride$submissionType,
	numAssays = content.pride$numAssays,
	instrumentNames = pleural2single(content.pride$instrumentNames),
	projectTags = pleural2single(content.pride$projectTags),
	doi = null2na(content.pride$doi),
	#------
	# submitter details
	submitterName = formatSubmitter(content.pride$submitter),
	submitterEmail = content.pride$submitter$email,
	submitterAffiliation = content.pride$submitter$affiliation,
	submissionDate = content.pride$submissionDate,
	#------
	# lab head details
	labHeadName = formatLabHeads(content.pride$labHeads),
	labHeadEmail = content.pride$labHeads[[1]]$email,
	labHeadAffiliation = content.pride$labHeads[[1]]$affiliation,
	#------
	# experimental details
	reanalysis = null2na(content.pride$reanalysis),
	experimentTypes = pleural2single(content.pride$experimentTypes),
	quantificationMethods = pleural2single(content.pride$quantificationMethods),
	keywords = bindKeyWords(content.pride$keywords),
	sampleProcessingProtocol = content.pride$sampleProcessingProtocol,
	dataProcessingProtocol = content.pride$dataProcessingProtocol,
	#------
	# project descriptions
	projectDescription = content.pride$projectDescription,
	referencesDesc = content.pride$references[[1]]$desc,
	referencesIDs = pleural2single(content.pride$references[[1]][2]),
	stringsAsFactors = FALSE
	)
	return(df.pride)
}
#-------
# getAllPrideProject helper function
# convert list to data.frame format
prideMiniList2DF <- function(prideMiniList){
	prideMiniDF <- data.frame(
		accession = prideMiniList$accession,
		title = prideMiniList$title,
		projectDescription = null2na(prideMiniList$projectDescription),
		publicationDate = prideMiniList$publicationDate,
		submissionType = prideMiniList$submissionType,
		numAssays = prideMiniList$numAssays,
		species = pleural2single(prideMiniList$species),
		tissues = pleural2single(prideMiniList$tissues),
		ptmNames = pleural2single(prideMiniList$ptmNames),
		instrumentNames = pleural2single(prideMiniList$instrumentNames),
		projectTags = pleural2single(prideMiniList$projectTags),
		stringsAsFactors =FALSE
	)
	return(prideMiniDF)
}
#------
# prideAllList2DF
prideAllList2DF <- function(prideAllList){
	prideList <- lapply(prideAllList,prideMiniList2DF)
	prideDF <- plyr::ldply(prideList)
}
rintukutum/pRideMetadb documentation built on May 27, 2019, 9:09 a.m.