Man pages for PNNL-CompBio/amlresistancenetworks
Calculates networks that lead to AML resistance to drugs

buildFeatureMatrixbuildFeatureMatrix This function sits at the core of the...
clusterDrugFamilyEfficacyselects AUC data and molecular data nand builds heatmap of...
clusterSingleDrugEfficacyselects AUC data and molecular data nand builds heatmap of...
computeAUCCorValswhat molecules are
computeDiffExByDrugNots ure if this is used yet Currently deprecated
computeFoldChangePvalsReads in data frame and computes fold change
computeGSEAcompute gene set enrichment - osama's code wrapped in...
computeKSEAcompute kinase substrate enrichment - osama's code wrapped in...
computePhosphoChangesget ordered phospho sites
computePhosphoNetworkcomputePhosphoNetwork maps kinase activity to proteins in a...
computeProteinNetworkcomputeProteinNetwork
doRegularGoRuns regular bag of genes enrichment
doRegularKinRuns regular bag of genes enrichment
drugMolLogRegdrugMolLogReg Computes logistic regression based on AUC...
drugMolLogRegEvaldrugMolLogRegEval Computes logistic regression and evaluates...
drugMolRandomForestdrugMolRandomForest builds random forest predictor of...
drugMolRegressionworking on this function still The goal is to use a basic...
drugMolRegressionEvaldrugMolRegressionEval This is the primary function that runs...
findCandidatesThe goal is to pre filter features using limma, with the hope...
getCoClusteredProteinsgetCoClusteredProteins Designed to evaluate time-course data...
getCorrelatedProteinsGet correlated proteins Computes protein correlations with...
getCytokineSensDatagetCytokine data gets cytokine sensitivity data and metadata...
getFeaturesFromStringgetFeaturesFromString - separates out comma-delimited model...
getFeaturesFromStringdfgetFeaturesFromStringdf - separates out comma-delimited model...
getTimeCourseDatagetTimecourseData
limmaTwoFactorDEAnalysislimmaTwoFactorDEAnalysis uses Osama's code to compute de from...
manualDEAnalysiscompute manual lfc
mapPhosphoToKinasemapPhosphoToKInase reads in phospho data, looads of KSDB and...
miniForestminiForest Runds random forest on the table and molecular...
miniForestEvalminiForestEval
miniLogRminiDE Carries out differential expressiona nalysis using an...
miniLogREvalminiLogReval: Assesses the performance of building a logistic...
miniRegminiReg Runs lasso regression on a single feature from...
miniRegEvalminiRegEval Runs lasso regression on a single feature from...
plotAllAUCsplotall AUCS with clinical data what are we measuring here
plotCorrelationEnrichmentPlot using correlation enrichment from leapR package. A...
plotCorrelationsByDrughow do we visualize the correlations of each drug/gene pair?
plotGSEAPlot using clusterProfiler. 3 GSEA plots are saved to the...
plotKinDatplotKinDat
plotOldGSEAPlot using clusterProfiler. 3 GSEA plots are saved to the...
plotProtsByMetricplotPRotsByMetric plots basal protein expression by metric...
plotSingleProteinplot single protein
querySynapseTablequery synapse table This is how you get data from the project
readAndTidyMetadatareads in metadata from excel spreadsheet and tidies it
readAndTidyPhosphoProtMeasuresreads and tidies phosphoprotein measurements joins with...
readAndTidyProtMeasuresreads and tidies protein measurements joins with metadata...
readAndTidyQuizMetadatareads in metadata from excel spreadsheet and tidies it
readAndTidyQuizPhosphoProtMeasuresreads and tidies phosphoprotein measurements joins with...
readAndTidyQuizProtMeasuresreads and tidies protein measurements joins with metadata...
readAndTidySensMetadatareads and tidies experiment 11 metadata
readAndTidySensPhosMeasuresreads and tidies phosphototeomic data for experimnet 11
readAndTidySensProtMeasurereads and tidies bulk proteomic data for experiment 11
readAndTidyUncorrectedQuizPhosphoMeasuresreads and tidies uncorrected phosphoprotein measurements...
reverselog_transUsed to make reversed logarithmic scales
synapseLoginLogs into Synapse using local information
synapseStoreSynapse store
synTableStoreSynapse table store REQUIRES PANDAS ON YOUR PYTHON PATH
synTableUpdatesynTableUpdate Removes all rows from table and replaces
testDatatestData
PNNL-CompBio/amlresistancenetworks documentation built on Feb. 8, 2025, 11:27 a.m.