Man pages for JEFworks/HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data
| calcAlleleCnvBoundaries | Use HMM to identify potential CNV boundaries based on... |
| calcAlleleCnvProb | Calculate posterior probability of CNVs using allele data |
| calcCombCnvProb | Calculate posterior probability of CNVs using normalized... |
| calcGexpCnvBoundaries | HMM to identify CNV boundaries using normalized gene... |
| calcGexpCnvProb | Calculate posterior probability of CNVs using normalized... |
| cov.sc | Coverage for putative heterozygous variants inferred from the... |
| getAlleleCount | Get alternative allele count for positions of interest |
| getCellAlleleCount | Get alternative allele count for positions of interest for... |
| getCoverage | Get coverage count for positions of interest |
| getHetRate | Helper function to get het rate from allele counts at a list... |
| getSnpMats | Helper function to get coverage and allele count matrices... |
| getSnpMats10X | Helper function to get coverage and allele count matrices... |
| gexp | Gene expression for cells from MGH31 from Patel et al. |
| HoneyBADGER_calcAlleleCnvBoundaries | Recursive HMM to identify CNV boundaries using allele data |
| HoneyBADGER_calcAlleleCnvProb | Calculate posterior probability of CNVs using allele data |
| HoneyBADGER_calcCombCnvProb | Calculate posterior probability of CNVs using normalized... |
| HoneyBADGER_calcGexpCnvBoundaries | Recursive HMM to identify CNV boundaries using normalized... |
| HoneyBADGER_calcGexpCnvProb | Calculate posterior probability of CNVs using normalized... |
| HoneyBADGER-class | A Reference Class to represent single-cell RNA-seq data for... |
| HoneyBADGER_plotAlleleProfile | Plot allele profile |
| HoneyBADGER_plotGexpProfile | Plot gene expression profile |
| HoneyBADGER_plotSmoothedAlleleProfile | Plot smoothed allele profile |
| HoneyBADGER_retestIdentifiedCnvs | Calculate posterior probability of CNVs for regions... |
| HoneyBADGER_setAlleleMats | Set allele count matrices, creates in-silico pooled single... |
| HoneyBADGER_setGeneFactors | Maps snps to genes |
| HoneyBADGER_setGexpDev | Set needed absolute gene expression deviance to be able to... |
| HoneyBADGER_setGexpMats | Set gene expression matrices, normalizes, and maps genes to... |
| HoneyBADGER_setMvFit | Model expected gene expression variance as a function of... |
| HoneyBADGER_summarizeResults | Summarize results |
| HoneyBADGER_visualizeResults | Plot posterior probability as heatmap |
| isHet | Helper function to determine heterzogosity at a position from... |
| isHetAlt | Alternate helper function to determine heterzogosity at a... |
| plotAlleleProfile | Plot allele profile |
| plotGexpProfile | Plot gene expression profile |
| r | Alternative allele count for putative heterozygous variants... |
| ref | Gene expression reference using normal cells from MGH31 from... |
| setAlleleMats | Functions related to allele model Set allele count matrices,... |
| setGeneFactors | Maps snps to genes |
| setGexpDev | Set needed absolute gene expression deviance to be able to... |
| setGexpMats | Functions related to gene expression model Set gene... |
| setMvFit | Model expected gene expression variance as a function of... |
| trimSnps | Function to filter out SNPs from ExAC database |
