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 |
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