Man pages for lgl15/cnmtf
Prioritisation of single nucleotide variants using Corrected non-negative matrix tri-factorisation
| about.cnmtf | Read me first!! |
| analyze.cnmtf | Analyze cNMTF results |
| annotate.results | Annotate prioritised SNVs |
| clus.membership | Calculate connectivity matrix |
| cnmtf | cNMTF algorithm |
| coding.scheme | Select genetic model for the genotyping data |
| consensus.clust | Find consensus clustering and SNV score |
| construct.Vo | Constructs the outcome matrix |
| construct.Wu | Constructs the SNV-SNV adjacency matrix |
| create.network | Constructs the SNV-SNV network |
| custom.venn | Plot Venn Diagrams |
| degree.distribution | Plot node degree of a network |
| delta.score | Delta score between clusters |
| hello | Hello, World! |
| hierarchical.clust | Hierarchical clustering from consensus connectivity matrices |
| initialise.UV | Initialising the low-rank matrices U and V |
| kernels.cnmtf | Calculates the kernel similarity matrix |
| manhattan.plot | Manhattan plot |
| manhattan.table | Manhattan table |
| mapply.snpt.synthetic.gwas | Simulate synthetic genotypes |
| neg.constrain | Constraining positive entries in a matrix |
| parameters.cnmtf | Optimal penalization paramaters |
| plot.clusters | Plot cNMTF clusters |
| plot.parameter | Plot penalization parameters |
| plot.pca | Plot of PCA for patients |
| pos.constrain | Constraining negative entries in a matrix |
| psvd.init | SVD Initialisation for NMF |
| R | Relationship matrix of SNVs and patients |
| rec.list | Recursive lists |
| regression.snps | Prioritise variants using regression models |
| rownet.hub | Creates edge list for the SNV-SNV network |
| score.cnmtf | Calculate Omega matrix |
| sd.plot | Plotting delta scores |
| sd.score | Calculate standardised delta score |
| snpt.synthetic.gwas | Simulate synthetic genotypes |
| synthetic.gwas | Simulate synthetic genotypes |
| tmap | Mapping table for SNVs |
