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)
}
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