Man pages for arnevpladsen/CARMA
Calculate CARMA scores
| binRegions | Define CARMA bins |
| binSegments | Split a segmented copy number profile into a set of... |
| CARMA | Calculate CARMA scores |
| carma.all | Calculate CARMA scores within a region |
| carma-package | Calculate CARMA scores |
| carma.S1 | Calculate CARMA score AMP |
| carma.S1 2 | Calculate CARMA score AMP |
| carma.S2 | Calculate CARMA score DEL |
| carma.S3 | Calculate CARMA score STP |
| carma.S4 | Calculate CARMA score CRV |
| carma.S5 | Calculate CARMA score LOH |
| carma.S5 2 | Calculate CARMA score LOH |
| carma.S6 | Calculate CARMA score ASM |
| center | Calculate median ploidy across the genome |
| combineTables | Combine CARMA score tables |
| continuousSegments | Make continuous segments and split segments spanning the... |
| formatPlotScores | Format CARMA scores for use in plotting functions |
| formatPlotSeg | Format copy number segments for use in plotting functions |
| genesCARMA | A function for mapping of CARMA scores to genes |
| getReference | Save CARMA input parameters |
| heatCol | Make continous heat map colors |
| hg19 | hg 19 chromosome arm start and end positions |
| hg19 2 | hg 19 chromosome arm start and end positions |
| hg19_genes | hg19 gene reference positions |
| hg38 | hg 38 chromosome arm start and end positions |
| hg38_genes | hg38 gene reference positions |
| normalizeCARMA | Normalize CARMA scores |
| plotDataset | Plot summary of CARMA scores across the entire dataset or... |
| plotSample | Plot sample specific CARMA scores |
| reformatCARMA | Reformat CARMA scores |
| splitTable | Split a CARMA score table |
| splitTable 2 | Split a CARMA score table |
| summaryCARMA | Make summary table of CARMA scores for all samples |
| test.data | Test data - copy number profiles |
| test.data 2 | Test data - copy number profiles |
| vectorToTable | Format CARMA scores for use in plotting function |
