Integration of Omics Data Using Linear Modeling


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Documentation for package ‘IntLIM’ version 0.1.0

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CorrHeatmap Plot correlation heatmap
CorrHeatmap_pdf Plot correlation heatmap in pdf
CreateIntLimObject Generic function to create constructor of MultiDataSet gene object
DistPvalues Visualize the distribution of unadjusted p-values from linear models
FilterData Filter input data by abundance values (gene and metabolite data) and number of missing values (metabolite data only).
getCommon Function that returns a list of all data for samples in common between metabolite and gene datasets
getGeneList Obtain lists of source IDs for inputting into RaMP or other pathway analysis program Requires sourceIDs and IDtypes Otherwise will output names given The IDtype should be as below +--+ | IDtype | +--+ | enzymeNomenclature | | ensembl | | entrez | | hmdb | | kegg | | uniprot | +--+
getMetabList Obtain lists of source IDs for inputting into RaMP or other pathway analysis program Requires sourceIDs and IDtypes Otherwise will output names given The IDtype should be as below +-+ | IDtype | +-+ | CAS | | chebi | | chemspider | | hmdb | | kegg | | LIPIDMAPS | | pubchem | +-+
getstatsOneLM Function that runs linear models for one gene vs all metabolites
HistogramGMPairs histogram of gene-metabolite pairs depending upon metabolite or gene
IntLimResults-class IntLimResults class
MetaboliteSet-class MetaboliteSet class extenstion for MultiDataSet object
OutputData Output data into individual CSV files. All data will be zipped into one file with all data.
OutputResults Output results into a zipped CSV file. Results include gene and metabolite pairs, along with model interaction p-values, and correlations in each group being evaluated.
PlotDistributions Get some stats after reading in data
PlotGMPair scatter plot of gene-metabolite pairs (based on user selection)
PlotPCA PCA plots of data for QC
ProcessResults Retrieve significant gene-metabolite pairs, based on adjusted p-values. For each gene-metabolite pair that is statistically significant, calculate the correlation within group1 (e.g. cancer) and the correlation within group2 (e.g. non-cancer). Users can then remove pairs with a difference in correlations between groups 1 and 2 less than a user-defined threshold.
pvalCorrVolcano 'volcano' plot (difference in correlations vs p-values) of all gene-metabolite pairs
ReadData Read in CSV file
RunIntLim Run linear models and retrieve relevant statistics
runIntLIMApp run shiny app
RunLM Function that runs linear models and returns interaction p-values.
ShowStats Get some stats after reading in data