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 |