Man pages for xlucpu/MOVICS
Multi-Omics integration and VIsualization in Cancer Subtyping
| affinityMatrix | affinityMatrix |
| calcPhenotype | Calculates phenotype from microarray data. |
| cgp2016ExprRma | GDSC 2016 gene expression data |
| classifySamples | Dichotimize a training expression set and fit a logistic... |
| compAgree | Comparison of agreement between two subtypes |
| compClinvar | Comparison of clinical variables |
| compDrugsen | Comparison of drug sensitivity |
| compFGA | Comparison of fraction genome altered |
| compMut | Comparison of mutational frequency |
| compSurv | Comparison of prognosis by Kaplan-Meier survival curve |
| compTMB | Comparsion of total mutation burden |
| dist2 | dist2 |
| doVariableSelection | a function to do variable selection on expression matrices. |
| drugData2016 | GDSC 2016 drug data |
| estimateCI.pRRopheticCv | Confidence intervals from "pRRopheticCv" object. |
| estimateMeanPredictionError.pRRopheticCv | Mean prediction error from "pRRopheticCv" object. |
| estimateMedianPredictionError.pRRopheticCv | Median prediction error from "pRRopheticCv" object. |
| estimateRsqr.pRRopheticCv | R^2 from "pRRopheticCv" object. |
| getCGPinfo | Given a drug and tissue type, return CGP expression and drug... |
| getCIMLR | Get subtypes from CIMLR |
| getClustNum | Get estimation of optimal clustering number |
| getCOCA | Get subtypes from COCA |
| getConsensusClustering | Get subtypes from ConsensusClustering |
| getConsensusMOIC | Get subtypes from consensus clustering of multiple... |
| getElites | Get elites for clustering |
| getiClusterBayes | Get subtypes from iClusterBayes |
| getIntNMF | Get subtypes from IntNMF |
| getLRAcluster | Get subtypes from LRAcluster |
| getMoCluster | Get subtypes from MoCluster |
| getMoHeatmap | Get multi-omics comprehensive heatmap |
| getMOIC | Get subtypes from multi-omics integrative clustering |
| getNEMO | Get subtypes from NEMO |
| getPINSPlus | Get subtypes from PINSPlus |
| getPPV | Calculate PPV and NPV and a cutpoint from the training data. |
| getSilhouette | Get silhoutte plot from consensus clustering |
| getSNF | Get subtypes from SNF |
| getStdiz | Get standardized omics data |
| homogenizeData | Take two expression matrices and return homogenized versions... |
| LRAcluster | integrated analysis of cancer omics data by low-rank... |
| nemo.affinity.graph | NEMO affinity graph |
| nemo.clustering | NEMO clustering |
| nemo.num.clusters | NEMO num clusters |
| plot.pRRopheticCv | Plot "pRRopheticCv" object. |
| predictionAccuracyByCv | Cross validation on training dataset |
| pRRopheticCV | This function uses X fold cross validation on the TrainingSet... |
| pRRopheticLogisticPredict | Predict from the CGP data using a logistic model |
| pRRopheticPredict | Given a gene expression matrix, predict drug senstivity for a... |
| pRRopheticQQplot | Check the distribution of the drug response (IC50) data using... |
| quiet | Suppress function messages and Concatenate and Print (cat) |
| runDEA | Run differential expression analysis |
| runGSEA | Run identification of unique functional pathways |
| runGSVA | Run gene set variation analysis |
| runKappa | Run consistency evaluation using Kappa statistic |
| runMarker | Run identification of unique biomarkers |
| runNTP | Run nearest template prediction |
| runPAM | Run partition around medoids classifier |
| spectralClustering | Spectral clustering |
| summarizeGenesByMean | Take an expression matrix and if duplicate genes are... |
| summary.pRRopheticCv | Summary of "pRRopheticCv" object. |
| twoclassdeseq2 | Run two class comparison |
| twoclassedger | Run two class comparison |
| twoclasslimma | Run two class comparison |
