Man pages for sdchandra/CNAclinic
A Software Suite for Shallow Sequencing Copy Number Analysis
| callData-CNAclinicData-method | Call segments as 'gain', 'loss' or 'neutral' |
| CNAclinicData | An S4 class to contain the copy number, segmentation and... |
| combineData-CNAclinicData-CNAclinicData-method | Combine the slots of two CNAclinicData objects |
| exportData | Export data |
| getGeneInfo | Get transcript and position information for NCBI Entrez gene... |
| optimalBinsize | Assess optimal genomic bin size to partition read counts. |
| plotMultiSampleData-CNAclinicData-method | Plots heat map of a cohort of samples |
| plotSampleData-CNAclinicData-method | plotSampleData |
| processForSegmentation | Process reads counts from BAM files to prepare input for... |
| runSegmentation | Run up to 4 different copy number segmentation algorithms. |
| statsCNA-CNAclinicData-method | Quantify and quality check copy-number profiles. |
| subsetData-CNAclinicData-method | Extract data belonging to a subset of samples in a CNAclinic... |
| summSegments-CNAclinicData-method | Summarise segments from multiple algorithms at every genomic... |
