Man pages for Fraternalilab/BrepConvert
BrepConvert: R package for gene conversion analysis of B cell repertoire
| adjustBroadPos | Give 'broad' start/end points of gene conversion events |
| batchConvertAnalysis | Annotating gene conversion events in BCR repertoire data. |
| blat | Function to run BLAT. |
| doBlat | Extract sequence stretches to be analysed using BLAT. |
| formatBlat | Function to format BLAT output |
| getAAGeneConversion | Translate amino acid sequences for gene conversion events |
| getBroadCDNA | Give 'broad' cDNA sequence of gene conversion events in the... |
| getCoverage | Count gene conversion events which cover/start at every DNA... |
| getEditDistance | Function to calculate Levenshtein distance between defined... |
| getIdenticalLength | Function to calculate the length of identical sequence... |
| getNarrowCDNA | Give 'narrow' cDNA sequence of gene conversion events in the... |
| getTopBlat | Function to rank and obtain donor pseudogenes which best... |
| mergeHits | Function to merge adjacent events explainable by the same... |
| plotCoverage | Histograms of gene conversion events |
| plotEvents | Visualise locations of gene conversion events |
| ScanGeneConversion | Wrapper function to scan and annotate gene conversion events |
