Man pages for macintyrelab/CNpare
Comparing tumour copy number profiles
| calculateSumOfPosteriors | Calculate sum of posteriors |
| CCLE_metadata | Metadata of the CCLE dataset |
| cells_mapping | Information of dataset from where genomic data of cell lines... |
| cells_segcn | Precomputed dataset of 1,417 human cancer cell line profiles. |
| CNconvert | A helper function for CNPlot_events |
| CNpare-package | CNpare: Comparing tumour copy number profiles |
| CNPlot_events | Visualization of two copy-number profiles |
| extractCopynumberFeatures | Extract features of copy number profiles |
| generateSampleByComponentMatrix | Get components per sample |
| getBinsStartsEnds | Get genomic positions of bins |
| getBPnum | Get counts of brekpoints per 10Mb |
| getCentromereDistCounts | Get the breakpoint count per chromosome arm |
| getChangepointCN | Get difference in copy number between adjacent segments |
| getCINProfiles | Get profiles with detectable CIN |
| getCINSamp | elect samples with CIN |
| getClusterSamples | Get list of samples included in the closest cluster to the... |
| getCN | Get copy numbers |
| getCNbins | Get copy-number per bins |
| getCNbins.bin | Get copy-number in a bin |
| getCNbins.sample | Get copy-number per bins in a sample |
| getDifference | Calculation of the extent of differences between two profiles |
| getInputmatrix | Get input data as matrix |
| getNewSegments | Create new segments for unifying profiles in a specific... |
| getPloidy | Calculation of ploidy status |
| getProfiles | Add profiles in a list |
| getSampNames | Get sample names |
| getSegRounded | Round copy-number values of segments |
| getSegsize | Get length of segments |
| getSegTable | Get segmented table of each sample |
| getSimilarities | Get similarity metrics |
| getSimilarities.sample | Get similarity metrics per sample |
| getTopHit | Get top hits |
| getUnifiedCN | Get copy number values of each new unified segment from a... |
| lengthChr | Length of chromosomes |
| lower_norm | Get lower normalized value |
| normaliseMatrix | Normalize matrix |
| pair_cosine | Calculation of cosine similarity |
| pair_euclidean | Calculation of euclidean distance |
| pair_manhattan | Calculation of manhattan distance |
| pair_pearson | Perform a pearson correlation test |
| plotClusters | Plots a scatter plots with samples clustered |
| plot_diffdensity | Density plot showing the distribution of genome differences |
| plot_simdensity | Density plot showing the distribution of similarities |
| quantifySignatures | Quantifying signatures |
| unifySegments | Alignment of genomic positions of segments |
