Man pages for JEFworks/badger
Bayesian approach for detecting copy number alterations from single cell RNA-seq data
| calcAlleleCnvProb | Run BADGER allele-only model to assess posterior probability... |
| calcCombCnvProb | Run BADGER combined model to assess posterior probability of... |
| calcErrorRate | Calculate effective error rate |
| calcGexpCnvProb | Run BADGER expression-only model to assess posterior... |
| clafProfile | Composite Minor Allele Frequency (CLAF) Profile plot |
| geneFactors | Returns a factor vector across pos (chr:pos vector)... |
| getAlleleCount | Get alternative allele count for positions of interest |
| getCoverage | Get coverage count for positions of interest |
| insideCnvs | Returns a vector of T/F depending on whether SNPs are in CNV... |
| mvFit | Estimate expression magnitude variance as a function of... |
| normalizedExpression | Normalize gene expression to a normal reference for... |
| plotExpHeatmap | Visualize expression heatmap by chromosome for... |
| pointsWithin | Determine if a point is within a range |
| pos2GRanges | From data frame of positions to GRanges object |
| range2GRanges | From data frame of ranges to GRanges object |
