Clean up code for bioconductor, function specific

[biwenzel]

for loops to apply if possible

• generateGraphsFromFASTA
• .generateQuantGraphs
• generateGraphsFromQuantData
• .addUniquenessAttributes
• .addAveragePepRatio
• .collapseEdgelistQuant
• .collapseEdgelist
• .convertToBipartiteGraph
• .digest2
• digestFASTA
• generateEdgelist
• .generateGraphsFromEdgelist
• .getProteinOrigin
• .isomorphicBipartite
• .directBipartiteGraph
• readMqPeptideTable
• aggregateReplicates
• .foldChange
• calculatePeptideRatios
• .generatePrototypeList
• .geomMean
• plotBipartiteGraph
• automatedAnalysisIteratedCi
• iterateOverCi
• errorEquation
• .minimizeSquaredError
• proteinElimination
• .calculateProteinNodeInfo
• .calculateSubgraphCharacteristics
• .calculateSummaryTable

catch errors and error messages

• generateGraphsFromFASTA
• .generateQuantGraphs
• generateGraphsFromQuantData
• .addUniquenessAttributes
• .addAveragePepRatio
• .collapseEdgelistQuant
• .collapseEdgelist
• .convertToBipartiteGraph
• .digest2
• digestFASTA
• generateEdgelist
• .generateGraphsFromEdgelist
• .getProteinOrigin
• .isomorphicBipartite
• .directBipartiteGraph
• readMqPeptideTable
• aggregateReplicates
• .foldChange
• calculatePeptideRatios
• .generatePrototypeList
• .geomMean
• plotBipartiteGraph
• automatedAnalysisIteratedCi
• iterateOverCi
• errorEquation
• .minimizeSquaredError
• proteinElimination
• .calculateProteinNodeInfo
• .calculateSubgraphCharacteristics
• .calculateSummaryTable

under 50 lines and 80 characters, idents = 4 space

• generateGraphsFromFASTA
• .generateQuantGraphs
• generateGraphsFromQuantData
• .addUniquenessAttributes
• .addAveragePepRatio
• .collapseEdgelistQuant
• .collapseEdgelist
• .convertToBipartiteGraph
• .digest2
• digestFASTA
• generateEdgelist
• .generateGraphsFromEdgelist
• .getProteinOrigin
• .isomorphicBipartite
• .directBipartiteGraph
• readMqPeptideTable
• aggregateReplicates
• .foldChange
• calculatePeptideRatios
• .generatePrototypeList
• .geomMean
• plotBipartiteGraph
• automatedAnalysisIteratedCi
• iterateOverCi
• errorEquation
• .minimizeSquaredError
• proteinElimination
• .calculateProteinNodeInfo
• .calculateSubgraphCharacteristics
• .calculateSummaryTable

Tests:

• tests for isomorphisms
• test directBipartiteGraph
• test for graph generation FASTA
• test for graph generation quant
• test digest
• test protein origin
• test plot graph
• test preprocess
• test quant
• test small helper
• test tables
• test attributes