Man pages for jyyulab/NetBID
Network-based Bayesian Inference of Drivers, version 2
| bid | Calculate Differential Expression (DE) or Differential... |
| cal.Activity | Calculate Activity Value for Each Driver |
| cal.Activity.GS | Calculate Activity Value for Gene Sets |
| combineDE | Combine Multiple Comparison Results from Differential... |
| combinePvalVector | Combine P Values Using Fisher's Method or Stouffer's Method |
| db.preload | Preload database files into R workspace for NetBID2 |
| draw.2D | Visualize Sample Clustering Result in 2D Plot |
| draw.2D.ellipse | Visualize Sample Clustering Result in 2D Plot with Ellipse |
| draw.2D.interactive | Visualize Sample Clustering Result in 2D Plot with... |
| draw.2D.text | Visualize Sample Clustering Result in 2D Plot with Sample... |
| draw.3D | Visualize Sample Clustering Result in 3D Plot |
| draw.bubblePlot | Heat Bubble Matrix Plot for Top Drivers in NetBID2 Analysis |
| draw.categoryValue | Scatter Box Plot of Driver's Expression Values and Activity... |
| draw.clustComp | Visualize Each Sample's Observed Label vs. Predicted Label in... |
| draw.combineDE | Plot for combined DE (differentiated expressed)/DA... |
| draw.emb.kmeans | Visualize the K-means Clustering Result by several dimension... |
| draw.eset.QC | QC plots for ExpressionSet class object. |
| draw.funcEnrich.bar | Bar Plot for Gene Set Enrichment Analysis Result |
| draw.funcEnrich.cluster | Cluster Plot for Gene Set Enrichment Analysis Result |
| draw.GSEA | GSEA (Gene Set Enrichment Analysis) Plot for one Gene Set or... |
| draw.GSEA.NetBID | Draw GSEA (gene set enrichment analysis) Plot with NetBID... |
| draw.GSEA.NetBID.GS | Draw GSEA (gene set enrichment analysis) Plot with NetBID... |
| draw.heatmap | Draw Heatmap Plot to Display the Expression Level or Activity... |
| draw.MICA | Draw Cluster Plot Using MICA (cluster algorithm) |
| draw.NetBID | Create Plot to show Differential Expression and Differential... |
| draw.network.QC | QC Tables and Plots for Network Object |
| draw.oncoprint | Draw Oncoprint Plot to display the mutation information |
| draw.targetNet | Target Network Structure Plot for One Driver |
| draw.targetNet.TWO | Target Ntwork Structure Plot for Two Drivers |
| draw.volcanoPlot | Draw Volcano Plot for Top DE (differentiated expressed) Genes... |
| funcEnrich.Fisher | Gene Set Enrichment Analysis by Fisher's Exact Test |
| funcEnrich.GSEA | Gene Set Enrichment Analysis by GSEA |
| generate.eset | Generate ExpressionSet Object |
| generate.masterTable | Generate the Master Table for Drivers |
| get.class.color | Create Color Codes for a Vector of Characters |
| get_clustComp | Get Score to Measure Similarity Between Observed... |
| getDE.BID.2G | Differential Expression Analysis and Differential Activity... |
| getDE.limma.2G | Differential Expression Analysis and Differential Activity... |
| get_IDtransfer | Creates Data Frame for ID Conversion |
| get_IDtransfer2symbol2type | Create Data Frame for ID Conversion With Biotype Information |
| get_IDtransfer_betweenSpecies | Create Data Frame for ID Conversion Between Species |
| get_int_group | Get interested phenotype groups from pData slot of the... |
| get_name_transfertab | Convert Original Gene ID into Target Gene ID |
| get_net2target_list | Convert Pairwise Network Data Frame to Driver-to-Target List |
| get_obs_label | Create a vector of each sample's selected phenotye... |
| get.SJAracne.network | Read SJARACNe Network Result and Return it as List Object |
| get.TF_SIG.list | Get Transcription Factor (TF) and Signaling Factor (SIG) List |
| gs.preload | Load MSigDB Database into R Workspace |
| IQR.filter | IQR (interquartile range) filter to extract genes from... |
| load.exp.GEO | Download Gene Expression Series From GEO Database with... |
| load.exp.RNASeq.demo | Load Gene Expression Set from RNA-Seq Results (demo version) |
| load.exp.RNASeq.demoSalmon | Load Gene Expression Set from Salmon Output (demo version) |
| merge_eset | Merge Two ExpressionSet Class Objects into One |
| merge_gs | Merge Selected Major GeneSets from MsigDB |
| merge_target_list | Merge Target Gene List for Two Drivers |
| merge_TF_SIG.AC | Merge Activity Values from TF (transcription factors)... |
| merge_TF_SIG.network | Merge TF (transcription factor) Network and Sig (signaling... |
| NetBID.analysis.dir.create | Manipulation of Working Directories for NetBID2 Driver... |
| NetBID.lazyMode.DriverEstimation | Lazy mode for NetBID2 driver estimation |
| NetBID.lazyMode.DriverVisualization | Lazy mode for NetBID2 result visualization |
| NetBID.loadRData | Reload Saved RData Created by 'NetBID.saveRData'. |
| NetBID.network.dir.create | Manipulation of Working Directories for NetBID2 Network... |
| NetBID.saveRData | Save Data Produced by Corresponding NetBID2 Pipeline Step. |
| out2excel | Save the Master Table into Excel File |
| processDriverProfile | Clean Activity-based profile |
| RNASeqCount.normalize.scale | Normalization of RNA-Seq Reads Count |
| SJAracne.prepare | Prepare Data Files for Running SJARACNe |
| test.targetNet.overlap | Test for Intersection of Target Genes between Two Drivers |
| update_eset.feature | Reassign featureData slot of ExpressionSet and Update feature... |
| update_eset.phenotype | Reassign the phenoData slot of ExpressionSet and Update... |
| update_SJAracne.network | Update Network List Object Using Constraints |
| z2col | Set Color Scale for Z Statistics Value |
